diff --git a/index.mdwn b/index.mdwn
index 717f931..5694454 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -51,6 +51,7 @@ See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a
 
 ### Recent news
 
+ * June 2017: Minor update to support the use of SAMtools version 1.3 or higher.
  * October 2015: Application note preprint deposited in [bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
  * October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
   released on Bioconductor.

diff --git a/scripts/clonotypeR b/scripts/clonotypeR
index a655325..7c7055f 100755
--- a/scripts/clonotypeR
+++ b/scripts/clonotypeR
@@ -52,6 +52,19 @@ function test_extract_dir {
 	fi
 }
 
+# There was a backward-incompatible change of syntax for "samtools sort" in version 1.3.
+# https://github.com/samtools/samtools/blob/develop/NEWS
+function samtools_sort {
+	samtools 2>&1 | grep Version | grep -q htslib
+	if [ $? -ne 0 ]
+	then
+		printf "Your samtools version is old; consider upgrading\n"
+		samtools sort - $1
+	else
+		samtools sort - -o $1.bam
+	fi
+}
+
 case $1 in
 	detect)
 		shift
@@ -62,7 +75,7 @@ case $1 in
 			LIBRARY=$(basename $FASTQ_FILE .fastq)
 			bwa bwasw -t${THREADS:-1} $CLONOTYPER_REFERENCE/V-C/index $FASTQ_FILE |
 				samtools view -Su - |
-				samtools sort - $EXTRACT_DIR/$LIBRARY
+				samtools_sort $EXTRACT_DIR/$LIBRARY
 			samtools index $EXTRACT_DIR/$LIBRARY.bam
 		done
 	;;

diff --git a/index.mdwn b/index.mdwn
index 70612c6..a26f91b 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -42,6 +42,7 @@ to try alternative solutions, you can have a look at
 [MiXCR](https://milaboratory.com/software/mixcr/),
 [LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
 [tcR](https://imminfo.github.io/tcr/),
+[TraCeR](https://github.com/Teichlab/tracer),
 [VDJviz](https://github.com/antigenomics/vdjviz), or
 [VDJtools](https://github.com/mikessh/vdjtools).
 See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.

diff --git a/index.mdwn b/index.mdwn
index 717f931..70612c6 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,6 +39,7 @@ to try alternative solutions, you can have a look at
 [Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
 [MiTCR](http://mitcr.milaboratory.com/),
 [MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
+[MiXCR](https://milaboratory.com/software/mixcr/),
 [LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
 [tcR](https://imminfo.github.io/tcr/),
 [VDJviz](https://github.com/antigenomics/vdjviz), or

diff --git a/index.mdwn b/index.mdwn
index 293d9aa..717f931 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -40,6 +40,7 @@ to try alternative solutions, you can have a look at
 [MiTCR](http://mitcr.milaboratory.com/),
 [MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
 [LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
+[tcR](https://imminfo.github.io/tcr/),
 [VDJviz](https://github.com/antigenomics/vdjviz), or
 [VDJtools](https://github.com/mikessh/vdjtools).
 See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.

diff --git a/index.mdwn b/index.mdwn
index 4745394..293d9aa 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,7 +39,8 @@ to try alternative solutions, you can have a look at
 [Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
 [MiTCR](http://mitcr.milaboratory.com/),
 [MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
-[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full), or
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full),
+[VDJviz](https://github.com/antigenomics/vdjviz), or
 [VDJtools](https://github.com/mikessh/vdjtools).
 See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
 

diff --git a/DESCRIPTION b/DESCRIPTION
index 34c27ab..eb10cc0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.11.1
+Version: 1.11.2
 Date: 2016-04-23
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 31dd866..34c27ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.11.0
+Version: 1.11.1
 Date: 2016-04-23
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 27b25a2..31dd866 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.10.0
+Version: 1.11.0
 Date: 2016-04-23
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 2f4b79c..27b25a2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.9.1
+Version: 1.10.0
 Date: 2016-04-23
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/ChangeLog b/ChangeLog
index 3fad651..460527f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,6 @@
+2016-04-23  Charles Plessy <plessy@riken.jp>
+	* Increment minor version number to trigger update.
+
 2016-04-17  Charles Plessy <plessy@riken.jp>
 	* Added citation information.
 	* Point URL to the Branchable homepage.
diff --git a/DESCRIPTION b/DESCRIPTION
index 1d65d56..2f4b79c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.9.0
-Date: 2016-04-17
+Version: 1.9.1
+Date: 2016-04-23
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences

diff --git a/NEWS b/NEWS
index 1f8f401..d26b239 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.10.0
+
+OTHER CHANGES
+
+    o   Minor metadata updates.
+
 Changes in version 1.8.0
 
 NEW FEATURES

diff --git a/DESCRIPTION b/DESCRIPTION
index cda02f5..1d65d56 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
 Version: 1.9.0
-Date: 2015-10-06
+Date: 2016-04-17
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences
@@ -20,4 +20,5 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
 VignetteBuilder: knitr
 Packaged: 2013-12-11 10:22:39 UTC; charles
 biocViews: Sequencing
+URL: http://clonotyper.branchable.com/
 BugReports: http://clonotyper.branchable.com/Bugs/

diff --git a/ChangeLog b/ChangeLog
index 06e2de0..3fad651 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+2016-04-17  Charles Plessy <plessy@riken.jp>
+	* Added citation information.
+	* Point URL to the Branchable homepage.
+
+2015-02-05  Charles Plessy <plessy@riken.jp>
+	* Aded the function private_clonotypes().
+
 2014-09-25  Charles Plessy <plessy@riken.jp>
 	* Version 1.3.2
 	* Import “methods” instead of depending on.

diff --git a/inst/CITATION b/inst/CITATION
new file mode 100644
index 0000000..52cdbf0
--- /dev/null
+++ b/inst/CITATION
@@ -0,0 +1,16 @@
+citEntry( entry       = "article"
+        , author      = "Plessy, Charles and Mariotti-Ferrandiz, Encarnita and Manabe, Ri-Ichiroh and Hori, Shohei"
+        , title       = "clonotypeR--high throughput analysis of T cell antigen receptor sequences"
+        , year        = "2015"
+        , doi         = "10.1101/028696"
+        , publisher   = "Cold Spring Harbor Labs Journals"
+        , abstract    = "Motivation The T cell receptors are expressed as millions of different rearrangements. Amplified as a complex mixture of PCR products, they can be sequenced directly on next-generation instruments without the need for cloning. This method is increasingly used to characterize, quantify and study these highly diverse receptors. Results We present here clonotypeR, a software package to identify and analyze antigen receptors from high-throughput sequence libraries. ClonotypeR is designed to process, organize and analyze very large numbers of sequences, in the order of millions, typically produced by Roche 454 or Illumina instruments, and is made of two parts. The first contains shell scripts and reference segment sequences to produce a data file where each line represents a the detection of a clonotype in a sequence read. The second part is a R module available from Bioconductor, to load and filter the data, and prepare clonotype abundance tables ready for analysis with third-party tools for differential representation analysis, sample clustering, etc. To analyze clonotype data at the nucleotide level, we introduce unique clonotype identifiers based on those developed by Yassai et al. (2009), that we corrected to avoid identifier collisions. Availability http://clonotyper.branchable.com (CC0 license)."
+        , URL         = "http://www.biorxiv.org/content/early/2015/10/08/028696"
+        , eprint      = "http://www.biorxiv.org/content/early/2015/10/08/028696.full.pdf"
+        , journal     = "bioRxiv"
+        , textVersion = paste( "clonotypeR--high throughput analysis of T cell antigen receptor sequences."
+                             , "Charles Plessy, Encarnita Mariotti-Ferrandiz, Ri-Ichiroh Manabe, Shohei Hori."
+                             , "bioRxiv doi: http://dx.doi.org/10.1101/028696"
+                             , "This article is a preprint and has not been peer-reviewed."
+                             )
+        )

diff --git a/index.mdwn b/index.mdwn
index 428ac8e..4745394 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -38,8 +38,9 @@ to try alternative solutions, you can have a look at
 [[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
 [Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
 [MiTCR](http://mitcr.milaboratory.com/),
-[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html), or
-[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full).
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html),
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full), or
+[VDJtools](https://github.com/mikessh/vdjtools).
 See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
 
 *clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).

diff --git a/index.mdwn b/index.mdwn
index 82bf104..428ac8e 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -37,8 +37,9 @@ RIKEN about shortcomings, limitations, or possible developments.  If you need
 to try alternative solutions, you can have a look at
 [[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
 [Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
-[MiTCR](http://mitcr.milaboratory.com/), or
-[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
+[MiTCR](http://mitcr.milaboratory.com/),
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html), or
+[LymAnalyzer](http://nar.oxfordjournals.org/content/44/4/e31.full).
 See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
 
 *clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).

diff --git a/references/README.mdwn b/references/README.mdwn
index a256479..d357a9d 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -9,8 +9,10 @@ The references sequences are [TRA@.gb][Mmus_TRA], [TRB@.gb][Mmus_TRB] and
 files with full information from the NCBI's website, select _Show sequence_ and
 _GenBank (full)_ as shown in the panels below.
 
-![How to select "Show sequence"](NCBI_Show_sequence.png)
-![How to select "GenBank (full)"](NCBI_Save_GenBank_full.png)
+[[!img NCBI_Show_sequence.png alt='How to select "Show sequence"' link='no']]
+![](NCBI_Show_sequence.png)
+[[!img NCBI_Save_GenBank_full.png alt='How to select "GenBank (full)"' link='no']]
+![](NCBI_Save_GenBank_full.png)
 
 The *V*, *(D)*, *J* and *C* segments were extracted with the command `make
 gb2fa`, wich uses the the [extractfeat][] program of the EMBOSS package. 

diff --git a/references/TRG@.gb b/references/TRG@.gb
index 9d48faf..ff43dad 100644
--- a/references/TRG@.gb
+++ b/references/TRG@.gb
@@ -1,4 +1,4 @@
-LOCUS       NG_007033             179435 bp    DNA     linear   CON 03-NOV-2013
+LOCUS       NG_007033             179435 bp    DNA     linear   CON 29-DEC-2013
 DEFINITION  Mus musculus T cell receptor gamma chain (Tcrg) on chromosome 13.
 ACCESSION   NG_007033
 VERSION     NG_007033.1  GI:159120306
@@ -46,14 +46,15 @@ REFERENCE   4  (bases 1 to 179435)
   REMARK    GeneRIF: Gamma delta receptor loss in T-cells are involved in hair
             cycling defects.
 REFERENCE   5  (bases 1 to 179435)
-  AUTHORS   Jeong,S.P., Kang,J.A. and Park,S.G.
-  TITLE     Intestinal intraepithelial TCRgammadelta(+) T cells are activated
-            by normal commensal bacteria
-  JOURNAL   J. Microbiol. 50 (5), 837-841 (2012)
-   PUBMED   23124753
-  REMARK    GeneRIF: TCRgammadelta(+) T cell population attached to the
-            intestinal lumen is constitutively activated by normal commensal
-            bacteria.
+  AUTHORS   Laird,R.M., Wolf,B.J., Princiotta,M.F. and Hayes,S.M.
+  TITLE     gammadelta T cells acquire effector fates in the thymus and
+            differentiate into cytokine-producing effectors in a Listeria model
+            of infection independently of CD28 costimulation
+  JOURNAL   PLoS ONE 8 (5), E63178 (2013)
+   PUBMED   23671671
+  REMARK    GeneRIF: Data indicate that CD28 is dispensable for gammadelta
+            effector T cell development and differentiation.
+            Publication Status: Online-Only
 REFERENCE   6  (bases 1 to 179435)
   AUTHORS   Johnson,K.R. and Davisson,M.T.
   TITLE     A multipoint genetic linkage map of mouse chromosome 18
@@ -114,8 +115,8 @@ COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
             publications that are available for this gene. Please see the Gene
             record to access additional publications.
 PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
-            1-61826             AC122849.4         140943-202768
-            61827-179435        AC146604.5         30325-147933
+            1-61826             AC071805.4         140943-202768
+            61827-179435        AC131072.5         30325-147933
 FEATURES             Location/Qualifiers
      source          1..179435
                      /organism="Mus musculus"
@@ -128,14 +129,14 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="TCRGV1S1; TCRGV2S1; TCRGV3S1; TCRGV5S3"
                      /note="T cell receptor gamma chain"
                      /db_xref="GeneID:110067"
-                     /db_xref="MGI:98623"
+                     /db_xref="MGI:MGI:98623"
      gene            501..951
                      /gene="Tcrg-V7"
                      /gene_synonym="TRGV7; Vg7"
                      /note="T cell receptor gamma, variable 7"
                      /db_xref="GeneID:21641"
                      /db_xref="IMGT/GENE-DB:TRGV7"
-                     /db_xref="MGI:98637"
+                     /db_xref="MGI:MGI:98637"
      CDS             join(501..543,645..951)
                      /gene="Tcrg-V7"
                      /gene_synonym="TRGV7; Vg7"
@@ -143,7 +144,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:21641"
                      /db_xref="IMGT/GENE-DB:TRGV7"
-                     /db_xref="MGI:98637"
+                     /db_xref="MGI:MGI:98637"
      V_segment       join(501..543,645..951)
                      /gene="Tcrg-V7"
                      /gene_synonym="TRGV7; Vg7"
@@ -154,7 +155,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma, variable 4"
                      /db_xref="GeneID:21638"
                      /db_xref="IMGT/GENE-DB:TRGV4"
-                     /db_xref="MGI:98634"
+                     /db_xref="MGI:MGI:98634"
      CDS             join(7440..7551,7659..7965)
                      /gene="Tcrg-V4"
                      /gene_synonym="AI528624; TRGV4; Vg4"
@@ -162,7 +163,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:21638"
                      /db_xref="IMGT/GENE-DB:TRGV4"
-                     /db_xref="MGI:98634"
+                     /db_xref="MGI:MGI:98634"
      V_segment       join(7440..7551,7659..7965)
                      /gene="Tcrg-V4"
                      /gene_synonym="AI528624; TRGV4; Vg4"
@@ -173,7 +174,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma, variable 6"
                      /db_xref="GeneID:21640"
                      /db_xref="IMGT/GENE-DB:TRGV6"
-                     /db_xref="MGI:98636"
+                     /db_xref="MGI:MGI:98636"
      CDS             join(12827..12920,13077..13388)
                      /gene="Tcrg-V6"
                      /gene_synonym="TRGV6"
@@ -181,7 +182,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:21640"
                      /db_xref="IMGT/GENE-DB:TRGV6"
-                     /db_xref="MGI:98636"
+                     /db_xref="MGI:MGI:98636"
      V_segment       join(12827..12920,13077..13388)
                      /gene="Tcrg-V6"
                      /gene_synonym="TRGV6"
@@ -192,7 +193,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma, variable 5"
                      /db_xref="GeneID:21639"
                      /db_xref="IMGT/GENE-DB:TRGV5"
-                     /db_xref="MGI:98635"
+                     /db_xref="MGI:MGI:98635"
      CDS             join(14737..14779,14887..15184)
                      /gene="Tcrg-V5"
                      /gene_synonym="TRGV5"
@@ -200,7 +201,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:21639"
                      /db_xref="IMGT/GENE-DB:TRGV5"
-                     /db_xref="MGI:98635"
+                     /db_xref="MGI:MGI:98635"
      V_segment       join(14737..14779,14887..15184)
                      /gene="Tcrg-V5"
                      /gene_synonym="TRGV5"
@@ -211,7 +212,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma joining 1"
                      /db_xref="GeneID:100126431"
                      /db_xref="IMGT/GENE-DB:TRGJ1"
-                     /db_xref="MGI:4440480"
+                     /db_xref="MGI:MGI:4440480"
      CDS             32802..32861
                      /gene="Trgj1"
                      /gene_synonym="Gm17003"
@@ -219,7 +220,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:100126431"
                      /db_xref="IMGT/GENE-DB:TRGJ1"
-                     /db_xref="MGI:4440480"
+                     /db_xref="MGI:MGI:4440480"
      J_segment       32802..32861
                      /gene="Trgj1"
                      /gene_synonym="Gm17003"
@@ -230,7 +231,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma, constant 1"
                      /db_xref="GeneID:107573"
                      /db_xref="IMGT/GENE-DB:TRGC1"
-                     /db_xref="MGI:98625"
+                     /db_xref="MGI:MGI:98625"
      CDS             join(36562..36891,38323..38367,38935..39077)
                      /gene="Tcrg-C1"
                      /gene_synonym="Cgamma1; Gm17004; TRGC1"
@@ -238,7 +239,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:107573"
                      /db_xref="IMGT/GENE-DB:TRGC1"
-                     /db_xref="MGI:98625"
+                     /db_xref="MGI:MGI:98625"
      C_region        join(36562..36891,38323..38367,38935..39077)
                      /gene="Tcrg-C1"
                      /gene_synonym="Cgamma1; Gm17004; TRGC1"
@@ -248,7 +249,8 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="Cgamma1; Gm17004; TRGC1"
                      /standard_name="PMC156147P8"
                      /db_xref="UniSTS:271385"
-     enhancer        41876..42875
+     regulatory      41876..42875
+                     /regulatory_class="enhancer"
                      /gene="Tcrg"
                      /gene_synonym="TCRGV1S1; TCRGV2S1; TCRGV3S1; TCRGV5S3"
                      /note="gamma 1 enhancer"
@@ -258,7 +260,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma, variable 3"
                      /db_xref="GeneID:21637"
                      /db_xref="IMGT/GENE-DB:TRGV3"
-                     /db_xref="MGI:98633"
+                     /db_xref="MGI:MGI:98633"
      CDS             join(65304..65349,65454..65760)
                      /gene="Tcrg-V3"
                      /gene_synonym="TCRGV5S3; TRGV3; vgamma3"
@@ -266,7 +268,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:21637"
                      /db_xref="IMGT/GENE-DB:TRGV3"
-                     /db_xref="MGI:98633"
+                     /db_xref="MGI:MGI:98633"
      V_segment       join(65304..65349,65454..65760)
                      /gene="Tcrg-V3"
                      /gene_synonym="TCRGV5S3; TRGV3; vgamma3"
@@ -277,7 +279,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor gamma joining 3"
                      /db_xref="GeneID:100126432"
                      /db_xref="IMGT/GENE-DB:TRGJ3"
-                     /db_xref="MGI:4439528"
+                     /db_xref="MGI:MGI:4439528"
      CDS             79576..79635
                      /gene="Trgj3"
                      /gene_synonym="Gm16604"
@@ -285,7 +287,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1

(Diff truncated)

diff --git a/references/TRB@.gb b/references/TRB@.gb
index 0f9255e..f4d8b3c 100644
--- a/references/TRB@.gb
+++ b/references/TRB@.gb
@@ -1,4 +1,4 @@
-LOCUS       NG_006980             668076 bp    DNA     linear   CON 05-NOV-2013
+LOCUS       NG_006980             668076 bp    DNA     linear   CON 05-NOV-2015
 DEFINITION  Mus musculus T cell receptor beta chain (Tcrb) on chromosome 6.
 ACCESSION   NG_006980
 VERSION     NG_006980.1  GI:158037406
@@ -9,74 +9,88 @@ SOURCE      Mus musculus (house mouse)
             Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
             Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus.
 REFERENCE   1  (bases 1 to 668076)
-  AUTHORS   Hess,C., Winkler,A., Lorenz,A.K., Holecska,V., Blanchard,V.,
-            Eiglmeier,S., Schoen,A.L., Bitterling,J., Stoehr,A.D., Petzold,D.,
-            Schommartz,T., Mertes,M.M., Schoen,C.T., Tiburzy,B., Herrmann,A.,
-            Kohl,J., Manz,R.A., Madaio,M.P., Berger,M., Wardemann,H. and
-            Ehlers,M.
-  TITLE     T cell-independent B cell activation induces immunosuppressive
-            sialylated IgG antibodies
-  JOURNAL   J. Clin. Invest. 123 (9), 3788-3796 (2013)
-   PUBMED   23979161
+  AUTHORS   Mallis RJ, Bai K, Arthanari H, Hussey RE, Handley M, Li Z,
+            Chingozha L, Duke-Cohan JS, Lu H, Wang JH, Zhu C, Wagner G and
+            Reinherz EL.
+  TITLE     Pre-TCR ligand binding impacts thymocyte development before
+            alphabetaTCR expression
+  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 112 (27), 8373-8378 (2015)
+   PUBMED   26056289
+  REMARK    GeneRIF: Data show that the pre-T-cell receptor (preTCR), a
+            pTalpha-beta heterodimer appearing before alphabetaTCR expression,
+            directs initial phase of repertoire selection.
 REFERENCE   2  (bases 1 to 668076)
-  AUTHORS   Hickey,A.J., Lin,J.S., Kummer,L.W., Szaba,F.M., Duso,D.K.,
-            Tighe,M., Parent,M.A. and Smiley,S.T.
-  TITLE     Intranasal prophylaxis with CpG oligodeoxynucleotide can protect
-            against Yersinia pestis infection
-  JOURNAL   Infect. Immun. 81 (6), 2123-2132 (2013)
-   PUBMED   23545300
+  AUTHORS   Bergot AS, Chaara W, Ruggiero E, Mariotti-Ferrandiz E, Dulauroy S,
+            Schmidt M, von Kalle C, Six A and Klatzmann D.
+  TITLE     TCR sequences and tissue distribution discriminate the subsets of
+            naive and activated/memory Treg cells in mice
+  JOURNAL   Eur. J. Immunol. 45 (5), 1524-1534 (2015)
+   PUBMED   25726757
+  REMARK    GeneRIF: in deep- versus superficial lymph nodes, TCR-beta deep
+            sequencing revealed diversified naive Treg-cell and
+            activated-memory Treg-cell repertoires
 REFERENCE   3  (bases 1 to 668076)
-  AUTHORS   Archer,N.K., Harro,J.M. and Shirtliff,M.E.
-  TITLE     Clearance of Staphylococcus aureus nasal carriage is T cell
-            dependent and mediated through interleukin-17A expression and
-            neutrophil influx
-  JOURNAL   Infect. Immun. 81 (6), 2070-2075 (2013)
-   PUBMED   23529621
+  AUTHORS   Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG,
+            Montpellier B, Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel
+            MS and Guidos CJ.
+  TITLE     IL-7 coordinates proliferation, differentiation and Tcra
+            recombination during thymocyte beta-selection
+  JOURNAL   Nat. Immunol. 16 (4), 397-405 (2015)
+   PUBMED   25729925
+  REMARK    GeneRIF: IL-7 critically acts cooperatively with signaling via the
+            pre-TCR and Notch1 to coordinate proliferation, differentiation and
+            TCRalpha recombination during beta-selection.
 REFERENCE   4  (bases 1 to 668076)
-  AUTHORS   Larson,R.P., Comeau,M.R. and Ziegler,S.F.
-  TITLE     Cutting edge: allergen-specific CD4 T cells respond indirectly to
-            thymic stromal lymphopoietin to promote allergic responses in the
-            skin
-  JOURNAL   J. Immunol. 190 (9), 4474-4477 (2013)
-   PUBMED   23543759
+  AUTHORS   Guenova E, Skabytska Y, Hoetzenecker W, Weindl G, Sauer K, Tham M,
+            Kim KW, Park JH, Seo JH, Ignatova D, Cozzio A, Levesque MP, Volz T,
+            Koberle M, Kaesler S, Thomas P, Mailhammer R, Ghoreschi K, Schakel
+            K, Amarov B, Eichner M, Schaller M, Clark RA, Rocken M and
+            Biedermann T.
+  TITLE     IL-4 abrogates T(H)17 cell-mediated inflammation by selective
+            silencing of IL-23 in antigen-presenting cells
+  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 112 (7), 2163-2168 (2015)
+   PUBMED   25646481
 REFERENCE   5  (bases 1 to 668076)
-  AUTHORS   Brady,B.L., Rupp,L.J. and Bassing,C.H.
-  TITLE     Requirement for dicer in survival of proliferating thymocytes
-            experiencing DNA double-strand breaks
-  JOURNAL   J. Immunol. 190 (7), 3256-3266 (2013)
-   PUBMED   23427252
+  AUTHORS   Khairnar V, Duhan V, Maney SK, Honke N, Shaabani N, Pandyra AA,
+            Seifert M, Pozdeev V, Xu HC, Sharma P, Baldin F, Marquardsen F,
+            Merches K, Lang E, Kirschning C, Westendorf AM, Haussinger D, Lang
+            F, Dittmer U, Kuppers R, Recher M, Hardt C, Scheffrahn I,
+            Beauchemin N, Gothert JR, Singer BB, Lang PA and Lang KS.
+  TITLE     CEACAM1 induces B-cell survival and is essential for protective
+            antiviral antibody production
+  JOURNAL   Nat Commun 6, 6217 (2015)
+   PUBMED   25692415
+  REMARK    Publication Status: Online-Only
 REFERENCE   6  (bases 1 to 668076)
-  AUTHORS   Acha-Orbea,H., Scarpellino,L., Shakhov,A.N., Held,W. and
-            MacDonald,H.R.
+  AUTHORS   Acha-Orbea H, Scarpellino L, Shakhov AN, Held W and MacDonald HR.
   TITLE     Inhibition of mouse mammary tumor virus-induced T cell responses in
             vivo by antibodies to an open reading frame protein
   JOURNAL   J. Exp. Med. 176 (6), 1769-1772 (1992)
    PUBMED   1334118
 REFERENCE   7  (bases 1 to 668076)
-  AUTHORS   Mombaerts,P., Clarke,A.R., Rudnicki,M.A., Iacomini,J., Itohara,S.,
-            Lafaille,J.J., Wang,L., Ichikawa,Y., Jaenisch,R., Hooper,M.L. et
-            al.
+  AUTHORS   Mombaerts P, Clarke AR, Rudnicki MA, Iacomini J, Itohara S,
+            Lafaille JJ, Wang L, Ichikawa Y, Jaenisch R, Hooper ML et al.
   TITLE     Mutations in T-cell antigen receptor genes alpha and beta block
             thymocyte development at different stages
   JOURNAL   Nature 360 (6401), 225-231 (1992)
    PUBMED   1359428
   REMARK    Erratum:[Nature 1992 Dec 3;360(6403):491]
 REFERENCE   8  (bases 1 to 668076)
-  AUTHORS   Ossendorp,F., Jacobs,H., van der Horst,G., de Vries,E., Berns,A.
-            and Borst,J.
+  AUTHORS   Ossendorp F, Jacobs H, van der Horst G, de Vries E, Berns A and
+            Borst J.
   TITLE     T cell receptor-alpha beta lacking the beta-chain V domain can be
             expressed at the cell surface but prohibits T cell maturation
   JOURNAL   J. Immunol. 148 (12), 3714-3722 (1992)
    PUBMED   1351085
 REFERENCE   9  (bases 1 to 668076)
-  AUTHORS   Suzuki,M., Koseki,H., Mizutani,Y., Kuribayashi,K., Kanno,M. and
-            Taniguchi,M.
+  AUTHORS   Suzuki M, Koseki H, Mizutani Y, Kuribayashi K, Kanno M and
+            Taniguchi M.
   TITLE     Expansion of murine T cells bearing a unique T cell receptor
             beta-chain in Friend virus-induced tumor in situ
   JOURNAL   J. Immunol. 148 (9), 2968-2973 (1992)
    PUBMED   1374106
 REFERENCE   10 (bases 1 to 668076)
-  AUTHORS   Waters,S.H., O'Neil,J.J., Melican,D.T. and Appel,M.C.
+  AUTHORS   Waters SH, O'Neil JJ, Melican DT and Appel MC.
   TITLE     Multiple TCR V beta usage by infiltrates of young NOD mouse islets
             of Langerhans. A polymerase chain reaction analysis
   JOURNAL   Diabetes 41 (3), 308-312 (1992)
@@ -114,13 +128,13 @@ COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
             publications that are available for this gene. Please see the Gene
             record to access additional publications.
 PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
-            1-40285             AC161887.5         187467-227751
-            40286-148984        AC161768.25        87370-196068
-            148985-267619       AC153851.27        99220-217854
-            267620-433004       AC125228.4         96216-261600
-            433005-559515       AC158659.6         1-126511            c
-            559516-635734       AC153854.7         105046-181264
-            635735-668076       AC117678.16        48698-81039
+            1-40285             AC157861.5         187467-227751
+            40286-148984        AC131072.25        87370-196068
+            148985-267619       AC131072.27        99220-217854
+            267620-433004       AC065536.4         96216-261600
+            433005-559515       AC131072.6         1-126511            c
+            559516-635734       AC131072.7         105046-181264
+            635735-668076       AC065536.16        48698-81039
 FEATURES             Location/Qualifiers
      source          1..668076
                      /organism="Mus musculus"
@@ -133,14 +147,14 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="TCRbeta; Tib"
                      /note="T cell receptor beta chain"
                      /db_xref="GeneID:21577"
-                     /db_xref="MGI:98578"
+                     /db_xref="MGI:MGI:98578"
      gene            502..1091
                      /gene="Trbv1"
                      /gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
                      /note="T cell receptor beta, variable 1"
                      /db_xref="GeneID:621968"
                      /db_xref="IMGT/GENE-DB:TRBV1"
-                     /db_xref="MGI:98594"
+                     /db_xref="MGI:MGI:98594"
      CDS             join(502..556,797..1091)
                      /gene="Trbv1"
                      /gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
@@ -148,7 +162,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:621968"
                      /db_xref="IMGT/GENE-DB:TRBV1"
-                     /db_xref="MGI:98594"
+                     /db_xref="MGI:MGI:98594"
      V_segment       join(502..556,797..1091)
                      /gene="Trbv1"
                      /gene_synonym="621968; Gm6273; Tcrb-V2; TCRBV2S1"
@@ -158,7 +172,7 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="1700020H15; Tryx3"
                      /note="protease, serine 58"
                      /db_xref="GeneID:232717"
-                     /db_xref="MGI:3608323"
+                     /db_xref="MGI:MGI:3608323"
      mRNA            complement(join(4468..4717,4801..4940,6511..6767,
                      6933..7071,9260..9344,9478..9593))
                      /gene="Prss58"
@@ -167,7 +181,7 @@ FEATURES             Location/Qualifiers
                      /transcript_id="NM_175020.3"
                      /db_xref="GI:146198660"

(Diff truncated)

diff --git a/references/NCBI_Save_GenBank_full.png b/references/NCBI_Save_GenBank_full.png
new file mode 100644
index 0000000..9f7a6bd
Binary files /dev/null and b/references/NCBI_Save_GenBank_full.png differ
diff --git a/references/NCBI_Show_sequence.png b/references/NCBI_Show_sequence.png
new file mode 100644
index 0000000..22815c4
Binary files /dev/null and b/references/NCBI_Show_sequence.png differ
diff --git a/references/README.mdwn b/references/README.mdwn
index 8f7211a..a256479 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -5,9 +5,15 @@ Mus musculus
 ------------
 
 The references sequences are [TRA@.gb][Mmus_TRA], [TRB@.gb][Mmus_TRB] and
-[TRG@.gb][Mmus_TRG], downloaded in GenBank format from [RefSeq][].  The *V*, *(D)*, *J* and *C* segments were
-extracted with the command `make gb2fa`, wich uses the the [extractfeat][]
-program of the EMBOSS package. 
+[TRG@.gb][Mmus_TRG], downloaded in GenBank format from [RefSeq][].  To save the
+files with full information from the NCBI's website, select _Show sequence_ and
+_GenBank (full)_ as shown in the panels below.
+
+![How to select "Show sequence"](NCBI_Show_sequence.png)
+![How to select "GenBank (full)"](NCBI_Save_GenBank_full.png)
+
+The *V*, *(D)*, *J* and *C* segments were extracted with the command `make
+gb2fa`, wich uses the the [extractfeat][] program of the EMBOSS package. 
 
 This directory contains *V* and *J* segments aligned on conserved motifs in the
 files [[V.fa]] and [[J.fa]].  These alignments were made by hand using [[SeaView|doc/seaview]] and

diff --git a/references/TRA@.gb b/references/TRA@.gb
index f0e1f64..b51e0b6 100644
--- a/references/TRA@.gb
+++ b/references/TRA@.gb
@@ -1,4 +1,4 @@
-LOCUS       NG_007044            1797232 bp    DNA     linear   CON 08-JUL-2013
+LOCUS       NG_007044            1797232 bp    DNA     linear   CON 30-SEP-2015
 DEFINITION  Mus musculus T cell receptor alpha delta locus (Tcra/tcrd@) on
             chromosome 14.
 ACCESSION   NG_007044
@@ -10,7 +10,7 @@ SOURCE      Mus musculus (house mouse)
             Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
             Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus.
 REFERENCE   1  (bases 1 to 1797232)
-  AUTHORS   Takeshita,S., Toda,M. and Yamagishi,H.
+  AUTHORS   Takeshita S, Toda M and Yamagishi H.
   TITLE     Excision products of the T cell receptor gene support a progressive
             rearrangement model of the alpha/delta locus
   JOURNAL   EMBO J. 8 (11), 3261-3270 (1989)
@@ -97,14 +97,14 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="Tcralpha"
                      /note="T cell receptor alpha chain"
                      /db_xref="GeneID:21473"
-                     /db_xref="MGI:98553"
+                     /db_xref="MGI:MGI:98553"
      gene            501..1410
                      /gene="Trav1"
                      /gene_synonym="Gm13987; OTTMUSG00000015242"
                      /note="T cell receptor alpha variable 1"
                      /db_xref="GeneID:627171"
                      /db_xref="IMGT/GENE-DB:TRAV1"
-                     /db_xref="MGI:3651476"
+                     /db_xref="MGI:MGI:3651476"
      CDS             join(501..549,1128..1410)
                      /gene="Trav1"
                      /gene_synonym="Gm13987; OTTMUSG00000015242"
@@ -112,7 +112,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:627171"
                      /db_xref="IMGT/GENE-DB:TRAV1"
-                     /db_xref="MGI:3651476"
+                     /db_xref="MGI:MGI:3651476"
      V_segment       join(501..549,1128..1410)
                      /gene="Trav1"
                      /gene_synonym="Gm13987; OTTMUSG00000015242"
@@ -122,7 +122,7 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="MOR244-3; Mor83; Or83"
                      /note="olfactory receptor 1509"
                      /db_xref="GeneID:57271"
-                     /db_xref="MGI:3031343"
+                     /db_xref="MGI:MGI:3031343"
      mRNA            22927..23936
                      /gene="Olfr1509"
                      /gene_synonym="MOR244-3; Mor83; Or83"
@@ -130,7 +130,7 @@ FEATURES             Location/Qualifiers
                      /transcript_id="NM_020514.2"
                      /db_xref="GI:282394046"
                      /db_xref="GeneID:57271"
-                     /db_xref="MGI:3031343"
+                     /db_xref="MGI:MGI:3031343"
      STS             22927..23936
                      /gene="Olfr1509"
                      /gene_synonym="MOR244-3; Mor83; Or83"
@@ -146,7 +146,7 @@ FEATURES             Location/Qualifiers
                      /db_xref="GI:282394047"
                      /db_xref="CCDS:CCDS27060.1"
                      /db_xref="GeneID:57271"
-                     /db_xref="MGI:3031343"
+                     /db_xref="MGI:MGI:3031343"
                      /translation="MGALNQTRVTEFIFLGLTDNWVLEILFFVPFTVTYMLTLLGNFL
                      IVVTIVFTPRLHNPMYFFLSNLSFIDICHSSVTVPKMLEGLLLERKTISFDNCIAQLF
                      FLHLFACSEIFLLTIMAYDRYVAICIPLHYSNVMNMKVCVQLVFALWLGGTIHSLVQT
@@ -163,7 +163,7 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="Mor10; MOR244-2; MOR244-4; Or10"
                      /note="olfactory receptor 1508"
                      /db_xref="GeneID:57270"
-                     /db_xref="MGI:3031342"
+                     /db_xref="MGI:MGI:3031342"
      mRNA            complement(join(35255..36556,39430..39995))
                      /gene="Olfr1508"
                      /gene_synonym="Mor10; MOR244-2; MOR244-4; Or10"
@@ -172,7 +172,7 @@ FEATURES             Location/Qualifiers
                      /transcript_id="NM_020513.2"
                      /db_xref="GI:112821657"
                      /db_xref="GeneID:57270"
-                     /db_xref="MGI:3031342"
+                     /db_xref="MGI:MGI:3031342"
      STS             35562..36634
                      /gene="Tcra"
                      /gene_synonym="Tcralpha"
@@ -188,7 +188,7 @@ FEATURES             Location/Qualifiers
                      /db_xref="GI:10048450"
                      /db_xref="CCDS:CCDS27061.1"
                      /db_xref="GeneID:57270"
-                     /db_xref="MGI:3031342"
+                     /db_xref="MGI:MGI:3031342"
                      /translation="MEKAVLINETSVMSFRLTGLSTNPLVQMAVFFIFLIFYVLTLVG
                      NILIVITIIYDRRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDACVV
                      QMFFLHLFACTEIFLLTVMAYDRYVAICKPLQYMTIMNWKVCMMLAAALWTGGTIHSI
@@ -204,7 +204,7 @@ FEATURES             Location/Qualifiers
                      /gene_synonym="MOR244-1; Mor28; Or28"
                      /note="olfactory receptor 1507"
                      /db_xref="GeneID:57269"
-                     /db_xref="MGI:3031341"
+                     /db_xref="MGI:MGI:3031341"
      mRNA            complement(join(62469..63506,67663..68229))
                      /gene="Olfr1507"
                      /gene_synonym="MOR244-1; Mor28; Or28"
@@ -212,7 +212,7 @@ FEATURES             Location/Qualifiers
                      /transcript_id="NM_001170918.1"
                      /db_xref="GI:283135127"
                      /db_xref="GeneID:57269"
-                     /db_xref="MGI:3031341"
+                     /db_xref="MGI:MGI:3031341"
      mRNA            complement(62469..63580)
                      /gene="Olfr1507"
                      /gene_synonym="MOR244-1; Mor28; Or28"
@@ -220,7 +220,7 @@ FEATURES             Location/Qualifiers
                      /transcript_id="NM_020512.2"
                      /db_xref="GI:283135125"
                      /db_xref="GeneID:57269"
-                     /db_xref="MGI:3031341"
+                     /db_xref="MGI:MGI:3031341"
      STS             62469..63580
                      /gene="Tcra"
                      /gene_synonym="Tcralpha"
@@ -236,7 +236,7 @@ FEATURES             Location/Qualifiers
                      /db_xref="GI:283135126"
                      /db_xref="CCDS:CCDS27062.1"
                      /db_xref="GeneID:57269"
-                     /db_xref="MGI:3031341"
+                     /db_xref="MGI:MGI:3031341"
                      /translation="MEKAVLINQTSVMSFRLTGLSTNPKVQMAIFFIFLIFYVLTLVG
                      NILIVITIIHDHRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDDCVV
                      QIFFLHLFACTEIFLLTVMAYDRYVAICKPLRYMTIMNWKVCMVLGGAMWTAGTIHSI
@@ -254,7 +254,7 @@ FEATURES             Location/Qualifiers
                      /db_xref="GI:283135128"
                      /db_xref="CCDS:CCDS27062.1"
                      /db_xref="GeneID:57269"
-                     /db_xref="MGI:3031341"
+                     /db_xref="MGI:MGI:3031341"
                      /translation="MEKAVLINQTSVMSFRLTGLSTNPKVQMAIFFIFLIFYVLTLVG
                      NILIVITIIHDHRLHTPMYFFLSNLSFIDVCHSTVTVPKMLSDTFSEEKLISFDDCVV
                      QIFFLHLFACTEIFLLTVMAYDRYVAICKPLRYMTIMNWKVCMVLGGAMWTAGTIHSI
@@ -272,14 +272,14 @@ FEATURES             Location/Qualifiers
                      /note="predicted gene 9537"
                      /pseudo
                      /db_xref="GeneID:671621"
-                     /db_xref="MGI:3779947"
+                     /db_xref="MGI:MGI:3779947"
      gene            111186..113410
                      /gene="Gm7122"
                      /gene_synonym="EG633692"
                      /note="predicted pseudogene 7122"
                      /pseudo
                      /db_xref="GeneID:633692"
-                     /db_xref="MGI:3644290"
+                     /db_xref="MGI:MGI:3644290"
      gene            139827..140587
                      /gene="Trav2"
                      /gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -287,7 +287,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor alpha variable 2"
                      /db_xref="GeneID:100042372"
                      /db_xref="IMGT/GENE-DB:TRAV2"
-                     /db_xref="MGI:3642679"
+                     /db_xref="MGI:MGI:3642679"
      CDS             join(139827..139866,140298..140587)
                      /gene="Trav2"
                      /gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -296,7 +296,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:100042372"
                      /db_xref="IMGT/GENE-DB:TRAV2"
-                     /db_xref="MGI:3642679"
+                     /db_xref="MGI:MGI:3642679"
      V_segment       join(139827..139866,140298..140587)
                      /gene="Trav2"
                      /gene_synonym="ENSMUSG00000072561; ENSMUSG00000076759;
@@ -308,7 +308,7 @@ FEATURES             Location/Qualifiers
                      /note="T cell receptor alpha variable 3-1"
                      /db_xref="GeneID:667441"
                      /db_xref="IMGT/GENE-DB:TRAV3-1"
-                     /db_xref="MGI:3644489"
+                     /db_xref="MGI:MGI:3644489"
      CDS             join(153296..153421,153457..153747)
                      /gene="Trav3-1"
                      /gene_synonym="EG667441; Gm8635"
@@ -316,7 +316,7 @@ FEATURES             Location/Qualifiers
                      /codon_start=1
                      /db_xref="GeneID:667441"
                      /db_xref="IMGT/GENE-DB:TRAV3-1"
-                     /db_xref="MGI:3644489"
+                     /db_xref="MGI:MGI:3644489"
      V_segment       join(153296..153421,153457..153747)
                      /gene="Trav3-1"
                      /gene_synonym="EG667441; Gm8635"
@@ -328,7 +328,7 @@ FEATURES             Location/Qualifiers
                      /pseudo
                      /db_xref="GeneID:100042384"

(Diff truncated)

diff --git a/DESCRIPTION b/DESCRIPTION
index 83ba17e..cda02f5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.8.0
+Version: 1.9.0
 Date: 2015-10-06
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index b3405df..83ba17e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.1
+Version: 1.8.0
 Date: 2015-10-06
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/doc/workflow.mdwn b/doc/workflow.mdwn
index c8a42b0..90bea49 100644
--- a/doc/workflow.mdwn
+++ b/doc/workflow.mdwn
@@ -1,7 +1,7 @@
 clonotypeR's workflow
 =====================
 
-This workflow summarises the different commands to run.  Step-by-step examples using [[test data|doc/examples/with_test_data]] or the [[examples/GSE35626]] public dataset are also available for a more detailed explanation.
+This workflow summarises the different commands to run.  Step-by-step examples using [[test data|doc/examples/with_test_data]] or the [[examples/GSE35626]] public dataset are also available for a more detailed explanation.  See also the preprint of our [application note deposited in bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
 
 Data preparation in the command line
 ------------------------------------

diff --git a/index.mdwn b/index.mdwn
index 92fe6a2..82bf104 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -47,6 +47,7 @@ See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a
 
 ### Recent news
 
+ * October 2015: Application note preprint deposited in [bioRxiv](http://biorxiv.org/content/early/2015/10/08/028696).
  * October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
   released on Bioconductor.
  * 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.

diff --git a/.Rbuildignore b/.Rbuildignore
index 36312b8..13929dd 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
 Makefile
 ^references$
 ^scripts$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index edd4856..fcd14f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 .ikiwiki
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
index dbe503a..b3405df 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.0
-Date: 2014-09-25
+Version: 1.7.1
+Date: 2015-10-06
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences
@@ -20,3 +20,4 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
 VignetteBuilder: knitr
 Packaged: 2013-12-11 10:22:39 UTC; charles
 biocViews: Sequencing
+BugReports: http://clonotyper.branchable.com/Bugs/
diff --git a/NEWS b/NEWS
index 4b9b4a2..1f8f401 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.8.0
+
+NEW FEATURES
+
+    o   Added a “private_clonotypes” function.
+
 Changes in version 1.4.0
 
 BUG FIXES
diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
index 48e28d8..e8eec4e 100644
--- a/R/private_clonotypes.R
+++ b/R/private_clonotypes.R
@@ -1,3 +1,19 @@
+#' private_clonotypes
+#' 
+#' List clonotypes found exclusively in one library.
+#' 
+#' @param ... Library names.
+#' @param data A clonotype table.
+#' 
+#' @return A vector of clonotype names.
+#' 
+#' @seealso \code{\link{clonotype_table}}
+#' 
+#' @examples
+#' clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+#' clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+#' private_clonotypes("C", data=clonotypes)
+
 private_clonotypes <- function (..., data) {
 
 libs <- c(...)
@@ -8,7 +24,7 @@ if ( ! is.character(libs) ) stop (
 )
 
 if ( ! is.data.frame(data) ) stop (
-	"Second argument must be a data frame of clonotypes."
+	"Data argument must be a data frame of clonotypes."
 )
 
 if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
diff --git a/man/private_clonotypes.Rd b/man/private_clonotypes.Rd
new file mode 100644
index 0000000..9fdd23b
--- /dev/null
+++ b/man/private_clonotypes.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/private_clonotypes.R
+\name{private_clonotypes}
+\alias{private_clonotypes}
+\title{private_clonotypes}
+\usage{
+private_clonotypes(..., data)
+}
+\arguments{
+\item{...}{Library names.}
+
+\item{data}{A clonotype table.}
+}
+\value{
+A vector of clonotype names.
+}
+\description{
+List clonotypes found exclusively in one library.
+}
+\examples{
+clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+private_clonotypes("C", data=clonotypes)
+}
+\seealso{
+\code{\link{clonotype_table}}
+}
+

diff --git a/DESCRIPTION b/DESCRIPTION
index 4e3e018..b3405df 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.7.0
-Date: 2014-09-25
+Version: 1.7.1
+Date: 2015-10-06
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences

diff --git a/NEWS b/NEWS
index 4b9b4a2..1f8f401 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.8.0
+
+NEW FEATURES
+
+    o   Added a “private_clonotypes” function.
+
 Changes in version 1.4.0
 
 BUG FIXES

diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
index 48e28d8..e8eec4e 100644
--- a/R/private_clonotypes.R
+++ b/R/private_clonotypes.R
@@ -1,3 +1,19 @@
+#' private_clonotypes
+#' 
+#' List clonotypes found exclusively in one library.
+#' 
+#' @param ... Library names.
+#' @param data A clonotype table.
+#' 
+#' @return A vector of clonotype names.
+#' 
+#' @seealso \code{\link{clonotype_table}}
+#' 
+#' @examples
+#' clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+#' clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+#' private_clonotypes("C", data=clonotypes)
+
 private_clonotypes <- function (..., data) {
 
 libs <- c(...)
@@ -8,7 +24,7 @@ if ( ! is.character(libs) ) stop (
 )
 
 if ( ! is.data.frame(data) ) stop (
-	"Second argument must be a data frame of clonotypes."
+	"Data argument must be a data frame of clonotypes."
 )
 
 if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
diff --git a/man/private_clonotypes.Rd b/man/private_clonotypes.Rd
new file mode 100644
index 0000000..9fdd23b
--- /dev/null
+++ b/man/private_clonotypes.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/private_clonotypes.R
+\name{private_clonotypes}
+\alias{private_clonotypes}
+\title{private_clonotypes}
+\usage{
+private_clonotypes(..., data)
+}
+\arguments{
+\item{...}{Library names.}
+
+\item{data}{A clonotype table.}
+}
+\value{
+A vector of clonotype names.
+}
+\description{
+List clonotypes found exclusively in one library.
+}
+\examples{
+clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
+clonotypes <- clonotype_table(levels(clonotypes$lib), data=clonotypes)
+private_clonotypes("C", data=clonotypes)
+}
+\seealso{
+\code{\link{clonotype_table}}
+}
+

diff --git a/.Rbuildignore b/.Rbuildignore
index 36312b8..13929dd 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@
 Makefile
 ^references$
 ^scripts$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index edd4856..fcd14f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 .ikiwiki
+.Rproj.user

diff --git a/DESCRIPTION b/DESCRIPTION
index dbe503a..4e3e018 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -20,3 +20,4 @@ Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
 VignetteBuilder: knitr
 Packaged: 2013-12-11 10:22:39 UTC; charles
 biocViews: Sequencing
+BugReports: http://clonotyper.branchable.com/Bugs/

diff --git a/index.mdwn b/index.mdwn
index e70b676..92fe6a2 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -8,7 +8,7 @@ in the order of millions, typically produced by Roche 454 instruments, and to
 prepare these sequences for differential expression analysis with the typical
 transcriptomics tools as well as for statistical analysis using existing [R][] packages.
 
-[Bioconductor]: http://www.bioconductor.org/packages/release/bioc/html/clonotypeR.html
+[Bioconductor]: https://www.bioconductor.org/packages/clonotypeR
 [R]: http://www.r-project.org/ "The R Project for Statistical Computing"
 
 *clonotypeR* is developed in the [RIKEN Yokohama Campus][RIKEN-Yokohama] by the

diff --git a/index.mdwn b/index.mdwn
index 5abd66f..e70b676 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -39,6 +39,7 @@ to try alternative solutions, you can have a look at
 [Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
 [MiTCR](http://mitcr.milaboratory.com/), or
 [MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
+See also the [OMICtool](http://omictools.com/rep-seq-c424-p1.html) website for a longer list of repertoire tools.
 
 *clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
 

diff --git a/index.mdwn b/index.mdwn
index 7099cc2..5abd66f 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -36,8 +36,9 @@ Plessy|http://genome.gsc.riken.jp/osc/english/members/Charles_Plessy.html]] at
 RIKEN about shortcomings, limitations, or possible developments.  If you need
 to try alternative solutions, you can have a look at
 [[IMGTHighV-QUEST|http://www.imgt.org/IMGTindex/IMGTHighV-QUEST.html]],
-[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"), or
-[MiTCR](http://mitcr.milaboratory.com/).
+[Decombinator](http://pubmed.gov/23303508 "Bioinformatics. 2013 Mar 1;29(5):542-50"),
+[MiTCR](http://mitcr.milaboratory.com/), or
+[MIGEC](http://migec.readthedocs.org/en/latest/cdrblast.html).
 
 *clonotypeR* is placed in the [public domain](http://creativecommons.org/publicdomain/zero/1.0/).
 

diff --git a/DESCRIPTION b/DESCRIPTION
index f304114..dbe503a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.5.0
+Version: 1.7.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 2f1eddb..dbe503a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.6.0
+Version: 1.7.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index f304114..2f1eddb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.5.0
+Version: 1.6.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn b/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn
new file mode 100644
index 0000000..b0afa07
--- /dev/null
+++ b/Bugs/Yassai_ID_should_have_no_codon_ID_in_absence_of_non-templated_codons..mdwn
@@ -0,0 +1,6 @@
+<pre>
+> yassai_identifier(c(V="TRAV14N-1", J="TRAJ56", dna="GCAGCTACTGGAGGCAATAATAAGCTGACT", pep="AATGGNNKLT"))
+[1] "aa.1A14N1A56L10"
+</pre>
+
+Should be `aa.A14N1A56L10`.

diff --git a/TODO.mdwn b/TODO.mdwn
index 525db48..82495ae 100644
--- a/TODO.mdwn
+++ b/TODO.mdwn
@@ -44,3 +44,11 @@ compare the number of lines to what is expected.
 Support extraction of barcoded reads.
 
 Report the number of V segments found after `clonotypeR detect`.
+
+Clonotype algebra, like in:
+
+<pre>
+`+.clonotypeList` <- function(X, Y) structure( union(X, Y),     class='clonotypeList')
+`^.clonotypeList` <- function(X, Y) structure( intersect(X, Y), class='clonotypeList')
+`-.clonotypeList` <- function(X, Y) structure( setdiff(X, Y),   class='clonotypeList')
+</pre>

diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
new file mode 100644
index 0000000..48e28d8
--- /dev/null
+++ b/R/private_clonotypes.R
@@ -0,0 +1,28 @@
+private_clonotypes <- function (..., data) {
+
+libs <- c(...)
+otherLibs <- setdiff(colnames(data), libs)
+
+if ( ! is.character(libs) ) stop (
+	"First argument must be a character vector of library names."
+)
+
+if ( ! is.data.frame(data) ) stop (
+	"Second argument must be a data frame of clonotypes."
+)
+
+if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
+	paste("Unknown library: ", libs[ ! libs %in% colnames(data) ],".", sep='', collapse=' ')
+)
+
+clonotypenames <- rownames(data)
+
+# drop=FALSE otherwise rowSums fails when there is only one column.
+
+expressedInLibs   <- rowSums(data[, libs     , drop=FALSE]) >  0
+absentInOtherLibs <- rowSums(data[, otherLibs, drop=FALSE]) == 0
+
+return(
+	clonotypenames[ expressedInLibs & absentInOtherLibs ]
+)
+}
diff --git a/man/unique_clonotypes.Rd b/man/unique_clonotypes.Rd
index 7e5fff9..2a4d865 100644
--- a/man/unique_clonotypes.Rd
+++ b/man/unique_clonotypes.Rd
@@ -16,10 +16,6 @@ clonotype_table.
   \item{data}{The name of the clonotype_table where the data is stored.}
 }
 
-\details{
-Uses the table called \dQuote{clonotypes} by default.
-}
-
 \value{
 Character vector of clonotype names.  Their order follows the original row name
 order of the clonotype_table.

diff --git a/R/private_clonotypes.R b/R/private_clonotypes.R
new file mode 100644
index 0000000..48e28d8
--- /dev/null
+++ b/R/private_clonotypes.R
@@ -0,0 +1,28 @@
+private_clonotypes <- function (..., data) {
+
+libs <- c(...)
+otherLibs <- setdiff(colnames(data), libs)
+
+if ( ! is.character(libs) ) stop (
+	"First argument must be a character vector of library names."
+)
+
+if ( ! is.data.frame(data) ) stop (
+	"Second argument must be a data frame of clonotypes."
+)
+
+if ( FALSE %in% ( libs %in% colnames(data) ) ) stop (
+	paste("Unknown library: ", libs[ ! libs %in% colnames(data) ],".", sep='', collapse=' ')
+)
+
+clonotypenames <- rownames(data)
+
+# drop=FALSE otherwise rowSums fails when there is only one column.
+
+expressedInLibs   <- rowSums(data[, libs     , drop=FALSE]) >  0
+absentInOtherLibs <- rowSums(data[, otherLibs, drop=FALSE]) == 0
+
+return(
+	clonotypenames[ expressedInLibs & absentInOtherLibs ]
+)
+}

diff --git a/man/unique_clonotypes.Rd b/man/unique_clonotypes.Rd
index 7e5fff9..2a4d865 100644
--- a/man/unique_clonotypes.Rd
+++ b/man/unique_clonotypes.Rd
@@ -16,10 +16,6 @@ clonotype_table.
   \item{data}{The name of the clonotype_table where the data is stored.}
 }
 
-\details{
-Uses the table called \dQuote{clonotypes} by default.
-}
-
 \value{
 Character vector of clonotype names.  Their order follows the original row name
 order of the clonotype_table.

diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index 3a2b487..bbdd8a2 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -2,8 +2,6 @@
 
 _Page in construction…_
 
-<span style="background: red; font-family: monospace">TTT</span>
-
 [SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
 user interface for multiple sequence alignment and molecular phylogeny”.  In
 addition to the traditional display of nucleotides, it can color the alignment

diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index 5c99ac4..3a2b487 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -12,13 +12,19 @@ very useful for manual alignemnt of _V_ and _J_ segments.
 
 ### Nucleotide view
 
+J segments must be aligned on the `FGxG` motif, but in the default view it is 
+not very obvious to see.  Switch to the codon view or the aminoacid view.
+
 [[!img SeaView_nucleotides.png alt="SeaView displaying colored nucleotides."]]
 
 ### Codon view
 
+Here, the `FGxG` motif stands out like for example “<span style="background: red; font-family: monospace">TTC</span><span style="background: lime; font-family: monospace">GGT</span><span style="background: olive; font-family: monospace">CAT</span><span style="background: lime; font-family: monospace">GGA</span>”.  This mode is very useful for finding the relevant reading frame, by adding or removing gaps before the first nucleotide.
+
 [[!img SeaView_codons.png alt="SeaView displaying colored codons."]]
 
 ### Aminoacid view
 
-[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]
+This mode is very useful for aligning in-frame sequences, checking the final alignment, and spotting easily the stop codons in pseudogenised segments. 
 
+[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]

diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index b40f1c6..5c99ac4 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -2,6 +2,8 @@
 
 _Page in construction…_
 
+<span style="background: red; font-family: monospace">TTT</span>
+
 [SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
 user interface for multiple sequence alignment and molecular phylogeny”.  In
 addition to the traditional display of nucleotides, it can color the alignment

diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
index c0fb06e..b40f1c6 100644
--- a/doc/seaview.mdwn
+++ b/doc/seaview.mdwn
@@ -14,7 +14,7 @@ very useful for manual alignemnt of _V_ and _J_ segments.
 
 ### Codon view
 
-[[!img SeaView_codons.png alt="SeaView displaying colored codons."]
+[[!img SeaView_codons.png alt="SeaView displaying colored codons."]]
 
 ### Aminoacid view
 

diff --git a/references/README.mdwn b/references/README.mdwn
index 4f98128..8f7211a 100644
--- a/references/README.mdwn
+++ b/references/README.mdwn
@@ -10,7 +10,7 @@ extracted with the command `make gb2fa`, wich uses the the [extractfeat][]
 program of the EMBOSS package. 
 
 This directory contains *V* and *J* segments aligned on conserved motifs in the
-files [[V.fa]] and [[J.fa]].  These alignments were made by hand using [SeaView][] and
+files [[V.fa]] and [[J.fa]].  These alignments were made by hand using [[SeaView|doc/seaview]] and
 may need to be revised when the reference sequences change.
 
 [Mmus_TRA]: http://www.ncbi.nlm.nih.gov/nuccore/NG_007044 (Mus musculus T cell receptor alpha delta locus (Tcra/tcrd@) on chromosome 14)

diff --git a/doc/seaview.mdwn b/doc/seaview.mdwn
new file mode 100644
index 0000000..c0fb06e
--- /dev/null
+++ b/doc/seaview.mdwn
@@ -0,0 +1,22 @@
+# Alignment of V and J segements with SeaView.
+
+_Page in construction…_
+
+[SeaView](http://doua.prabi.fr/software/seaview) is a “multiplatform, graphical
+user interface for multiple sequence alignment and molecular phylogeny”.  In
+addition to the traditional display of nucleotides, it can color the alignment
+by codons, or display the DNA sequence translated as protein.  This makes it
+very useful for manual alignemnt of _V_ and _J_ segments.
+
+### Nucleotide view
+
+[[!img SeaView_nucleotides.png alt="SeaView displaying colored nucleotides."]]
+
+### Codon view
+
+[[!img SeaView_codons.png alt="SeaView displaying colored codons."]
+
+### Aminoacid view
+
+[[!img SeaView_aminoacids.png alt="SeaView displaying colored aminoacids translated from the DNA sequences."]]
+
diff --git a/doc/seaview/SeaView_aminoacids.png b/doc/seaview/SeaView_aminoacids.png
new file mode 100644
index 0000000..929bf6f
Binary files /dev/null and b/doc/seaview/SeaView_aminoacids.png differ
diff --git a/doc/seaview/SeaView_codons.png b/doc/seaview/SeaView_codons.png
new file mode 100644
index 0000000..3d7ebd4
Binary files /dev/null and b/doc/seaview/SeaView_codons.png differ
diff --git a/doc/seaview/SeaView_nucleotides.png b/doc/seaview/SeaView_nucleotides.png
new file mode 100644
index 0000000..3d2bd23
Binary files /dev/null and b/doc/seaview/SeaView_nucleotides.png differ

diff --git a/index.mdwn b/index.mdwn
index f5ecc8b..7099cc2 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,8 @@ to try alternative solutions, you can have a look at
 
 ### Recent news
 
+ * October 2014: New stable version [1.4](http://www.bioconductor.org/packages/3.0/bioc/html/clonotypeR.html)
+  released on Bioconductor.
  * 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
  * March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
    released on Bioconductor.

diff --git a/DESCRIPTION b/DESCRIPTION
index ea7a4e3..f304114 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.4.0
+Version: 1.5.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index ea7a4e3..f304114 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.4.0
+Version: 1.5.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 1ef9e8b..ea7a4e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.2
+Version: 1.4.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index 1ef9e8b..ea7a4e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.2
+Version: 1.4.0
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/index.mdwn b/index.mdwn
index 357e7b9..f5ecc8b 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,7 @@ to try alternative solutions, you can have a look at
 
 ### Recent news
 
+ * 25 September 2014: version 1.3.2 compatible with EMBOSS 6.6.0.
  * March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
    released on Bioconductor.
  * 11 December 2013: Version 1.1.3 adding a `long` option to `yassai_identifier`, solving

diff --git a/ChangeLog b/ChangeLog
index 8c90a52..06e2de0 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+2014-09-25  Charles Plessy <plessy@riken.jp>
+	* Version 1.3.2
+	* Import “methods” instead of depending on.
+	* Corrected typos.
+
 2014-04-08  Charles Plessy <plessy@riken.jp>
 	* Version 1.1.6
 	* Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
@@ -8,7 +13,7 @@
 
 2014-03-05  Bioc admins
 	* Version 1.1.4.
-	* Change biocviews to “Sequencing”,
+	* Change biocviews to “Sequencing”.
 
 2013-12-11  Charles Plessy <plessy@riken>
 	* Committed 1.1.3 to Bioconductor.
diff --git a/DESCRIPTION b/DESCRIPTION
index 3370138..1ef9e8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.1
+Version: 1.3.2
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/NEWS b/NEWS
index e8067a7..4b9b4a2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.4.0
+
+BUG FIXES
+
+    o   Minor packaging corrections (NAMESPACE, etc.).
+
 Changes in version 1.2.0
 
 NEW FEATURES
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 32f4fe7..8679d56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -126,13 +126,13 @@ of the display).
 
 ### Detection of V segments
 
-Run the command `clonotyper detect A.fastq` in the same directory as a copy of
+Run the command `clonotypeR detect A.fastq` in the same directory as a copy of
 the file `A.fastq`.
 
 The result is stored in a temporary directory called `extraction_files`, that
 will be created if it does not already exist.
 
-`clonotyper detect` compares the sequences to the reference V segments using
+`clonotypeR detect` compares the sequences to the reference V segments using
 BWA, and produces output like the following.
 
     [bsw2_aln] read 2000 sequences/pairs (843395 bp)...
@@ -146,13 +146,13 @@ pairs in total.  There were 167 reference V segments, and the version number of
 BWA was `0.6.2-r126`.  The whole process took less than 10 seconds.
 
 Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect C.fastq` and `clonotyper detect C.fastq`.
+`clonotypeR detect B.fastq` and `clonotypeR detect C.fastq`.
 
 
 ### Extraction of CDR3 regions
 
-Run the command `clonotyper extract A` in the same directory as where you ran
-`clonotyper detect A.fastq`.  The result is a table stored in a directory
+Run the command `clonotypeR extract A` in the same directory as where you ran
+`clonotypeR detect A.fastq`.  The result is a table stored in a directory
 called `clonotypes`, that will be created if it does not already exist.
 
 The output is quite voluminous, and indicates which *V* / *J* combinations are

diff --git a/ChangeLog b/ChangeLog
index 8c90a52..06e2de0 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+2014-09-25  Charles Plessy <plessy@riken.jp>
+	* Version 1.3.2
+	* Import “methods” instead of depending on.
+	* Corrected typos.
+
 2014-04-08  Charles Plessy <plessy@riken.jp>
 	* Version 1.1.6
 	* Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
@@ -8,7 +13,7 @@
 
 2014-03-05  Bioc admins
 	* Version 1.1.4.
-	* Change biocviews to “Sequencing”,
+	* Change biocviews to “Sequencing”.
 
 2013-12-11  Charles Plessy <plessy@riken>
 	* Committed 1.1.3 to Bioconductor.
diff --git a/DESCRIPTION b/DESCRIPTION
index 3370138..1ef9e8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.1
+Version: 1.3.2
 Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/NEWS b/NEWS
index e8067a7..4b9b4a2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+Changes in version 1.4.0
+
+BUG FIXES
+
+    o   Minor packaging corrections (NAMESPACE, etc.).
+
 Changes in version 1.2.0
 
 NEW FEATURES

diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index bbbe652..fdea6b3 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -1,4 +1,4 @@
-In EMBOSS 6.6.6, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
+In EMBOSS 6.6.0, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
 
 <pre>
 echo -e '>A\nAAAAAA' > test-1.fa

diff --git a/scripts/VJsplit b/scripts/VJsplit
index 4b23919..b7502ea 100755
--- a/scripts/VJsplit
+++ b/scripts/VJsplit
@@ -72,7 +72,7 @@ do
     fi	
     echo -ne "\t$J_NAME\t" 1>&2
     J_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${J_LIB}-FGxG.fa:$J_NAME[:20] raw:stdout)
-    vectorstrip -auto \
+    EMBOSS_WARNING=FALSE vectorstrip -auto \
         -readfile N \
         -mismatch $VS_MISMATCH \
         -blinker $(seqret -filter $CLONOTYPER_REFERENCE/${J_LIB}-FGxG.fa:$J_NAME[:20] raw:stdout) \

diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
index 1648dce..7b7fef9 100644
--- a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
+++ b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
@@ -3,7 +3,7 @@
 [1] "tg.integer(0)A2A61L13"
 </pre>
 
-[[Done]] in  `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
+[[Done]] in  [[!commit 2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd]], by return an empty chain instead of `integer(0)` when receiving an empty chain.
 
 Result after correction:
 

diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
index 7cdfc91..e813803 100644
--- a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
+++ b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
@@ -45,7 +45,7 @@ TRAV14N-3      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This triggered an infinite loop when calling `is.germline()`.
 
-[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
+[[Done]] in [[!commit 42ab98729c5c77462b5929b00ee973074ae4c1c7]].
 
 Now the function should return as in the following example.
 

diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index 45abb7d..bbbe652 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -19,4 +19,4 @@ seqret test-1.fa:A stdout
 
 See also <http://lists.open-bio.org/pipermail/emboss/2014-June/008983.html>
 
-[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 055b6807d3f0e6fc6dda58f5699c6ac34fbc89c2]].
+[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 125524131bd57c084ee39374054b73784e6ae929]].

diff --git a/shortcuts.mdwn b/shortcuts.mdwn
index ca529c2..0cd4821 100644
--- a/shortcuts.mdwn
+++ b/shortcuts.mdwn
@@ -64,6 +64,8 @@ This page controls what shortcut links the wiki supports.
 * [[!shortcut name=freebsdwiki url="http://wiki.freebsd.org/%s"]]
 * [[!shortcut name=hackage url="http://hackage.haskell.org/package/%s"]]
 
+* [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]]
+
 To add a new shortcut, use the `shortcut`
 [[ikiwiki/directive]]. In the url, "%s" is replaced with the
 text passed to the named shortcut, after [[!wikipedia url_encoding]]

diff --git a/shortcuts.mdwn b/shortcuts.mdwn
new file mode 100644
index 0000000..ca529c2
--- /dev/null
+++ b/shortcuts.mdwn
@@ -0,0 +1,83 @@
+[[!if test="enabled(shortcut)"
+     then="This wiki has shortcuts **enabled**."
+     else="This wiki has shortcuts **disabled**."]]
+
+Some examples of using shortcuts include:
+
+	\[[!google foo]]
+	\[[!wikipedia War_of_1812]]
+	\[[!debbug 12345]]
+	Check the \[[!google ikiwiki desc="google search for %s"]].
+
+This page controls what shortcut links the wiki supports.
+
+* [[!shortcut name=google url="https://encrypted.google.com/search?q=%s"]]
+* [[!shortcut name=archive url="http://web.archive.org/*/%S"]]
+* [[!shortcut name=gmap url="https://maps.google.com/maps?q=%s"]]
+* [[!shortcut name=gmsg url="https://groups.google.com/groups?selm=%s"]]
+* [[!shortcut name=wikipedia url="https://en.wikipedia.org/wiki/%W"]]
+* [[!shortcut name=wikitravel url="https://wikitravel.org/en/%s"]]
+* [[!shortcut name=wiktionary url="https://en.wiktionary.org/wiki/%s"]]
+* [[!shortcut name=debbug url="http://bugs.debian.org/%S" desc="Debian bug #%s"]]
+* [[!shortcut name=deblist url="https://lists.debian.org/debian-%s" desc="debian-%s@lists.debian.org"]]
+* [[!shortcut name=debpkg url="http://packages.debian.org/%s"]]
+* [[!shortcut name=debpkgsid url="http://packages.debian.org/sid/%s"]]
+* [[!shortcut name=debpts url="http://packages.qa.debian.org/%s"]]
+* [[!shortcut name=debmsg url="https://lists.debian.org/msgid-search/%s"]]
+* [[!shortcut name=debrt url="https://rt.debian.org/Ticket/Display.html?id=%s"]]
+* [[!shortcut name=debss url="http://snapshot.debian.org/package/%s/"]]
+  * Usage: `\[[!debss package]]` or `\[[!debss package/version]]`.  See <http://snapshot.debian.org/> for details.
+* [[!shortcut name=debwiki url="https://wiki.debian.org/%S"]]
+* [[!shortcut name=fdobug url="https://bugs.freedesktop.org/show_bug.cgi?id=%s" desc="freedesktop.org bug #%s"]]
+* [[!shortcut name=fdolist url="http://lists.freedesktop.org/mailman/listinfo/%s" desc="%s@lists.freedesktop.org"]]
+* [[!shortcut name=gnomebug url="https://bugzilla.gnome.org/show_bug.cgi?id=%s" desc="GNOME bug #%s"]]
+* [[!shortcut name=linuxbug url="https://bugzilla.kernel.org/show_bug.cgi?id=%s" desc="Linux bug #%s"]]
+* [[!shortcut name=mozbug url="https://bugzilla.mozilla.org/show_bug.cgi?id=%s" desc="Mozilla bug #%s"]]
+* [[!shortcut name=gnulist url="https://lists.gnu.org/mailman/listinfo/%s" desc="%s@gnu.org"]]
+* [[!shortcut name=marcmsg url="http://marc.info/?i=%s"]]
+* [[!shortcut name=marclist url="http://marc.info/?l=%s"]]
+* [[!shortcut name=gmane url="http://dir.gmane.org/gmane.%s" desc="gmane.%s"]]
+* [[!shortcut name=gmanemsg url="http://mid.gmane.org/%s"]]
+* [[!shortcut name=cpan url="http://search.cpan.org/search?mode=dist&query=%s"]]
+* [[!shortcut name=ctan url="http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=%s"]]
+* [[!shortcut name=hoogle url="http://haskell.org/hoogle/?q=%s"]]
+* [[!shortcut name=iki url="http://ikiwiki.info/%S/"]]
+* [[!shortcut name=ljuser url="http://%s.livejournal.com/"]]
+* [[!shortcut name=rfc url="https://www.ietf.org/rfc/rfc%s.txt" desc="RFC %s"]]
+* [[!shortcut name=c2 url="http://c2.com/cgi/wiki?%s"]]
+* [[!shortcut name=meatballwiki url="http://www.usemod.com/cgi-bin/mb.pl?%s"]]
+* [[!shortcut name=emacswiki url="http://www.emacswiki.org/cgi-bin/wiki/%s"]]
+* [[!shortcut name=haskellwiki url="http://haskell.org/haskellwiki/%s"]]
+* [[!shortcut name=dict url="http://www.dict.org/bin/Dict?Form=Dict1&Strategy=*&Database=*&Query=%s"]]
+* [[!shortcut name=imdb url="http://imdb.com/find?q=%s"]]
+* [[!shortcut name=gpg url="http://pgpkeys.mit.edu:11371/pks/lookup?op=vindex&exact=on&search=0x%s"]]
+* [[!shortcut name=perldoc url="http://perldoc.perl.org/search.html?q=%s"]]
+* [[!shortcut name=whois url="http://reports.internic.net/cgi/whois?whois_nic=%s&type=domain"]]
+* [[!shortcut name=cve url="https://cve.mitre.org/cgi-bin/cvename.cgi?name=%s"]]
+* [[!shortcut name=flickr url="https://secure.flickr.com/photos/%s"]]
+* [[!shortcut name=man url="http://manpages.debian.org/%s"]]
+* [[!shortcut name=ohloh url="https://www.ohloh.net/p/%s"]]
+* [[!shortcut name=cpanrt url="https://rt.cpan.org/Ticket/Display.html?id=%s" desc="CPAN RT#%s"]]
+* [[!shortcut name=novellbug url="https://bugzilla.novell.com/show_bug.cgi?id=%s" desc="bug %s"]]
+* [[!shortcut name=ubupkg url="http://packages.ubuntu.com/%s"]]
+* [[!shortcut name=mozillazinekb url="http://kb.mozillazine.org/%s"]]
+* [[!shortcut name=freebsdwiki url="http://wiki.freebsd.org/%s"]]
+* [[!shortcut name=hackage url="http://hackage.haskell.org/package/%s"]]
+
+To add a new shortcut, use the `shortcut`
+[[ikiwiki/directive]]. In the url, "%s" is replaced with the
+text passed to the named shortcut, after [[!wikipedia url_encoding]]
+it, and '%S' is replaced with the raw, non-encoded text. 
+Additionally, `%W` is replaced with the text encoded just right for
+Wikipedia. The optional `desc` parameter controls the description of
+the link.
+
+Remember that the `name` you give the shortcut will become a new
+[[ikiwiki/directive]].  Avoid using a `name` that conflicts
+with an existing directive.  These directives also accept a `desc`
+parameter that will override the one provided at definition time.
+
+If you come up with a shortcut that you think others might find useful,
+consider contributing it to the [shortcuts page on the ikiwiki
+wiki](http://ikiwiki.info/shortcuts/), so that future versions of
+ikiwiki will include your shortcut in the standard underlay.

diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
index c95cbe8..45abb7d 100644
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -1,4 +1,4 @@
-The reason is the following bug in EMBOSS.
+In EMBOSS 6.6.6, sequence addresses with a dash and a colon cause are parsed as 'dbname:entry' instead of 'file:entry' when an appropriate directory name exists.
 
 <pre>
 echo -e '>A\nAAAAAA' > test-1.fa
@@ -16,3 +16,7 @@ seqret test-1.fa:A stdout
 # Error: Unable to read sequence 'test-1.fa:A'
 # Died: seqret terminated: Bad value for '-sequence' and no prompt
 </pre>
+
+See also <http://lists.open-bio.org/pipermail/emboss/2014-June/008983.html>
+
+[[Done]] with the following workaround: the directory `references/V` was renamed `references/V-C` in [[!commit 055b6807d3f0e6fc6dda58f5699c6ac34fbc89c2]].

diff --git a/doc/examples/with_test_data.mdwn b/doc/examples/with_test_data.mdwn
index 2808808..1dfa0dc 100644
--- a/doc/examples/with_test_data.mdwn
+++ b/doc/examples/with_test_data.mdwn
@@ -36,7 +36,7 @@ BWA, and produces output like the following.
     [bsw2_aln] read 2000 sequences/pairs (843395 bp)...
     [samopen] SAM header is present: 167 sequences.
     [main] Version: 0.6.2-r126
-    [main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V/index A.fastq
+    [main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V-C/index A.fastq
     [main] Real time: 1.099 sec; CPU: 8.225 sec
 
 This indicates that 2,000 reads have been processed, representing 843,395 base
diff --git a/html_doc/clonotypeR.html b/html_doc/clonotypeR.html
index aab33f8..3b262f0 100644
--- a/html_doc/clonotypeR.html
+++ b/html_doc/clonotypeR.html
@@ -392,7 +392,7 @@ BWA, and produces output like the following.</p>
 <pre><code>[bsw2_aln] read 2000 sequences/pairs (843395 bp)...
 [samopen] SAM header is present: 167 sequences.
 [main] Version: 0.6.2-r126
-[main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V/index A.fastq
+[main] CMD: bwa bwasw -t8 /usr/share/clonotypeR/references/V-C/index A.fastq
 [main] Real time: 1.099 sec; CPU: 8.225 sec
 </code></pre>
 
diff --git a/references/Makefile b/references/Makefile
index de53e5f..e775f3c 100644
--- a/references/Makefile
+++ b/references/Makefile
@@ -4,9 +4,9 @@ gb2fa: TRA@.gb TRB@.gb TRG@.gb
 	../scripts/gb2fa.bash
 
 bwa-index: V-C.fa
-	ln -s ../V-C.fa V/index
-	bwa index V/index
-	rm V/index
+	ln -s ../V-C.fa V-C/index
+	bwa index V-C/index
+	rm V-C/index
 
 degap: V-C.fa V_after_C.fa J_before_FGxG.fa J-FGxG.fa
 	for FA in V-C.fa V_after_C.fa J_before_FGxG.fa J-FGxG.fa ; do \
@@ -17,4 +17,4 @@ refresh-data:
 	R CMD BATCH --no-save J_before_FGxG.R
 
 clean:
-	@rm --force --verbose V/index.* V_after_C.Rout J_before_FGxG.Rout
+	@rm --force --verbose V-C/index.* V_after_C.Rout J_before_FGxG.Rout
diff --git a/references/V-C/index.amb b/references/V-C/index.amb
new file mode 100644
index 0000000..353dee2
--- /dev/null
+++ b/references/V-C/index.amb
@@ -0,0 +1 @@
+55126 169 0
diff --git a/references/V-C/index.ann b/references/V-C/index.ann
new file mode 100644
index 0000000..1d5538b
--- /dev/null
+++ b/references/V-C/index.ann
@@ -0,0 +1,339 @@
+55126 169 11
+0 TRAV1 (null)
+0 321 0
+0 TRAV2 (null)
+321 315 0
+0 TRAV3-1 (null)
+636 407 0
+0 TRAV4-1 (null)
+1043 317 0
+0 TRAV5-1 (null)
+1360 333 0
+0 TRAV6-1 (null)
+1693 327 0
+0 TRAV7-1 (null)
+2020 326 0
+0 TRAV6-2 (null)
+2346 330 0
+0 TRAV7D-2 (null)
+2676 327 0
+0 TRAV4D-2 (null)
+3003 321 0
+0 TRAV6D-3 (null)
+3324 327 0
+0 TRAV7D-3 (null)
+3651 327 0
+0 TRAV6D-4 (null)
+3978 329 0
+0 TRAV7D-4 (null)
+4307 327 0
+0 TRAV8D-1 (null)
+4634 327 0
+0 TRAV9D-1 (null)
+4961 327 0
+0 TRAV6D-5 (null)
+5288 327 0
+0 TRAV10D (null)
+5615 322 0
+0 TRAV6D-6 (null)
+5937 337 0
+0 TRAV13D-1 (null)
+6274 313 0
+0 TRAV15D-1/DV6D-1 (null)
+6587 336 0
+0 TRAV3D-2 (null)
+6923 328 0
+0 TRAV9D-2 (null)
+7251 330 0
+0 TRAV4D-3 (null)
+7581 318 0
+0 TRAV5D-2 (null)
+7899 281 0
+0 TRAV12D-2 (null)
+8180 327 0
+0 TRAV9D-3 (null)
+8507 330 0
+0 TRAV5D-3 (null)
+8837 212 0
+0 TRAV12D-3 (null)
+9049 331 0
+0 TRAV15D-2/DV6-2 (null)
+9380 326 0
+0 TRAV9D-4 (null)
+9706 220 0
+0 TRAV4D-4 (null)
+9926 319 0
+0 TRAV5D-4 (null)
+10245 337 0
+0 TRAV6D-7 (null)
+10582 324 0
+0 TRAV7D-6 (null)
+10906 324 0
+0 TRAV13D-3 (null)
+11230 327 0
+0 TRAV8D-2 (null)
+11557 327 0
+0 TRAV16D/DV11 (null)
+11884 312 0
+0 TRAV13D-4 (null)
+12196 327 0
+0 TRAV14D-3/DV8 (null)
+12523 351 0
+0 TRAV15D-3 (null)
+12874 218 0
+0 TRAV7N-4 (null)
+13092 326 0
+0 TRAV9N-1 (null)
+13418 321 0
+0 TRAV6N-5 (null)
+13739 325 0
+0 TRAV10N (null)
+14064 322 0
+0 TRAV6N-6 (null)
+14386 330 0
+0 TRAV11N (null)
+14716 333 0
+0 TRAV7N-5 (null)
+15049 319 0
+0 TRAV12N-1 (null)
+15368 330 0
+0 TRAV13N-1 (null)
+15698 321 0
+0 TRAV14N-1 (null)
+16019 354 0
+0 TRAV15N-1 (null)
+16373 336 0
+0 TRAV3N-2 (null)
+16709 324 0
+0 TRAV9N-2 (null)
+17033 330 0
+0 TRAV4N-3 (null)
+17363 321 0
+0 TRAV5N-2 (null)
+17684 277 0
+0 TRAV12N-2 (null)
+17961 333 0
+0 TRAV9N-3 (null)
+18294 330 0
+0 TRAV5N-3 (null)
+18624 270 0
+0 TRAV12N-3 (null)
+18894 336 0
+0 TRAV13N-2 (null)
+19230 321 0
+0 TRAV14N-2 (null)
+19551 354 0
+0 TRAV15N-2 (null)
+19905 336 0
+0 TRAV3N-3 (null)
+20241 333 0
+0 TRAV9N-4 (null)
+20574 330 0
+0 TRAV4N-4 (null)
+20904 321 0
+0 TRAV5N-4 (null)
+21225 337 0
+0 TRAV6N-7 (null)
+21562 357 0
+0 TRAV7N-6 (null)

(Diff truncated)

diff --git a/scripts/VJsplit b/scripts/VJsplit
index d1433f5..4b23919 100755
--- a/scripts/VJsplit
+++ b/scripts/VJsplit
@@ -49,7 +49,7 @@ do
     VECTORSTRIP_V_OUTFILE=$LIBRARY.${V_NAME//\//}.vectorstrip
   fi	
   echo -ne "$V_NAME\t" 1>&2
-  V_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${V_LIB}-C.fa:$V_NAME[-20:] raw:stdout)
+  V_SEQ=$(seqret -filter $CLONOTYPER_REFERENCE/${V_LIB}-C.fa:${V_NAME//\//?}[-20:] raw:stdout)
   # Encode the mapping quality and alignment score in the sequence name
   samtools view $EXTRACT_DIR/$LIBRARY.bam $V_NAME |
     perl -ne '($score) = /AS:i:(\d+)\t/ ; ($mapq) = (split)[4] ; print "AS_${score}_MQ_${mapq}_$_"' > $LIBRARY-${V_NAME//\//}-filtered.sam

diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 19da4f5..8679d56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -126,13 +126,13 @@ of the display).
 
 ### Detection of V segments
 
-Run the command `clonotyper detect A.fastq` in the same directory as a copy of
+Run the command `clonotypeR detect A.fastq` in the same directory as a copy of
 the file `A.fastq`.
 
 The result is stored in a temporary directory called `extraction_files`, that
 will be created if it does not already exist.
 
-`clonotyper detect` compares the sequences to the reference V segments using
+`clonotypeR detect` compares the sequences to the reference V segments using
 BWA, and produces output like the following.
 
     [bsw2_aln] read 2000 sequences/pairs (843395 bp)...
@@ -146,13 +146,13 @@ pairs in total.  There were 167 reference V segments, and the version number of
 BWA was `0.6.2-r126`.  The whole process took less than 10 seconds.
 
 Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect B.fastq` and `clonotyper detect C.fastq`.
+`clonotypeR detect B.fastq` and `clonotypeR detect C.fastq`.
 
 
 ### Extraction of CDR3 regions
 
-Run the command `clonotyper extract A` in the same directory as where you ran
-`clonotyper detect A.fastq`.  The result is a table stored in a directory
+Run the command `clonotypeR extract A` in the same directory as where you ran
+`clonotypeR detect A.fastq`.  The result is a table stored in a directory
 called `clonotypes`, that will be created if it does not already exist.
 
 The output is quite voluminous, and indicates which *V* / *J* combinations are

diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 32f4fe7..19da4f5 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -146,7 +146,7 @@ pairs in total.  There were 167 reference V segments, and the version number of
 BWA was `0.6.2-r126`.  The whole process took less than 10 seconds.
 
 Process the example libraries `B` and `C` similarly with the commands
-`clonotyper detect C.fastq` and `clonotyper detect C.fastq`.
+`clonotyper detect B.fastq` and `clonotyper detect C.fastq`.
 
 
 ### Extraction of CDR3 regions

diff --git a/DESCRIPTION b/DESCRIPTION
index 8e69f9b..3370138 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
 Version: 1.3.1
-Date: 2014-04-08
+Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences

diff --git a/DESCRIPTION b/DESCRIPTION
index 8e69f9b..3370138 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
 Version: 1.3.1
-Date: 2014-04-08
+Date: 2014-09-25
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
 Description: High throughput analysis of T cell antigen receptor sequences

diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 3de0e56..32f4fe7 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -57,7 +57,7 @@ library(clonotypeR)
 
 The data is a table of 120 clonotypes in the `extdata` folder of the package.
 The command `read_clonotypes` will parse it in a data frame.  The clonotypes
-are arbitrarly assigned to three libraries called `A`, `B`, and `C`.  The
+are arbitrarily assigned to three libraries called `A`, `B`, and `C`.  The
 `read_clonotypes` comments determines at load time if the peptidic sequence has
 a stop codon or is frame-shifted, and records the information in the
 `unproductive` column.
@@ -78,7 +78,7 @@ head(clonotype_table(levels(clonotypes$lib), "J", data=clonotypes))
 ```
 
 ClonotypeR provides other functions for further analysis.  `yassai_identifier`
-calculates a unique indentifier using the `V`, `J`, peptidic and nucleotidic
+calculates a unique identifier using the `V`, `J`, peptidic and nucleotidic
 information, following the work of [Yassai et al](http://dx.doi.org/10.1007/s00251-009-0383-x).
 
 ```{r yassai_identifier}
@@ -100,7 +100,7 @@ common_clonotypes(data=clonotypes)
 ```
 
 With deeper data, a typical follow-up would be to identify differentially
-represnted clonotypes between libraries, for instance with the `edgeR` package,
+represented clonotypes between libraries, for instance with the `edgeR` package,
 or to calculate distance between libraries, for instance with the
 `vegan` package.
 
@@ -109,7 +109,7 @@ Example data (3 x 2,000 reads)
 ------------------------------
 
 The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
+is a sub-sample of three sequence libraries of mouse T cell receptors &alpha; (2,000
 reads each) made on the 454 Titanium or the 454 junior platforms.  The original
 libraries will be deposited in public databanks after publication in a
 peer-reviewed journal.
@@ -210,7 +210,7 @@ The command `summary(clonotypes)` already provides useful information.
 summary(clonotypes)
 ```
 
-Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarly named `abc`. 
+Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarily named `abc`. 
 
 ```{r explore_data2}
 abc <- clonotype_table(c('A','B','C'), data=clonotypes)

diff --git a/Bugs.mdwn b/Bugs.mdwn
deleted file mode 100644
index 1106591..0000000
--- a/Bugs.mdwn
+++ /dev/null
@@ -1,12 +0,0 @@
-If you've found a bug in clonotypeR, post about it here. [[TODO]] items go
-elsewhere. Link items to [[Bugs/done]] when done.
-
-The [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]].
-You can use it to link to the commit that fixed the bug, as in `\[[!commit 7cf11805d84ff8dc6a537c17e73efa275077915d]]`.
-
-There are [[!pagecount pages="Bugs/* and !Bugs/done and !Bugs/discussion and 
-!link(patch) and !link(Bugs/done) and !Bugs/*/*"]] "open" bugs:
-
-[[!inline pages="Bugs/* and !Bugs/done and !Bugs/discussion and 
-!link(patch) and !link(Bugs/done) and !Bugs/*/*"
-actions=yes rootpage="Bugs" postformtext="Add a new bug titled:" show=0]]
diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
deleted file mode 100644
index 7cdfc91..0000000
--- a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
+++ /dev/null
@@ -1,55 +0,0 @@
-Problem
--------
-
-<pre>
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
-# takes ages
-
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAGCAACCGCAACTTCAAGTGGCCAGAAGCTGGTT", pep="AATATSSGQKLV"))
-## [1] "aTa.2A14N3A16L12"
-# returns immediately.
-</pre>
-
-
-Troubleshooting
----------------
-
-The problematic clonotype comes from read `GWYEMNS10GHZUF`.
-
-<pre>
-&#64;GWYEMNS10GHZUF
-gactAACTGGTACACAGCAGGTTCTGGGTTCTGGATGTGCAGGTACACCTTTAATATGGTCCCCTGGCCAAAAACCAGCTTCTGGCCACTTGAAGTTGCACAGAAGTAGGTGGCTGAGTCTCCAGGCTGAGAGTCTTTGATGTGCAAGGAGAGATTTTTCTCCCTTTTATTGAAGAAGATTGTGAATCGTCCATCTTCCTTTTTATCGGACACTGAACGTATGGCTATCAGGAGAGCAGGGCCTTCCCCAGGGAACTGCTGGTACCATGGGAAGTAGTCAAAAGCACTGTTCTCAtaactagcagttcagaattgcggtctctccttccccagactgtcagagattggagtcgtgggagacaaggcacacaggggataggngngnnnnnnnnnnnnn
-+
-FFF::;;FFFFFFFFIIIIHFFFHF666=&lt;FFGGDDDFFHFDIIIIIIIHHHIIIHFFFD54449662200001335&gt;&gt;AAABDFDDDFDDDFFFFFFFFFFFFFFFFFCCCCCFFFFFFFFFFFFDDBBBBB==110?&#64;&#64;&#64;&#64;&#64;&gt;4455BBA??3357;F4:::;;==D88?AA&lt;;:==BAAAA==??AAB&#64;AAA=&gt;&gt;&gt;222//02A8898BDDFFFDDFFFFFF666:DBAAAABB:::???DD;;;;D?????DDBA?&lt;&lt;&lt;&gt;&lt;&lt;&lt;&lt;000444&lt;8993222233393...:663322&lt;9233776899:;;963326755551111,,,,3313335333799.....23322666726;;;66772222,,,,47400!,!,!!!!!!!!!!!!!
-</pre>
-
-Here is the alignment made by clonotypeR
-
-<pre>
-GWYEMNS10GHZUF	16	TRAV14N-3	105	17	49S17M1I29M1I201M99S	*	0	0	NNNNNNNNNNNNNCNCNCCTATCCCCTGTGTGCCTTGTCTCCCACGACTCCAATCTCTGACAGTCTGGGGAAGGAGAGACCGCAATTCTGAACTGCTAGTTATGAGAACAGTGCTTTTGACTACTTCCCATGGTACCAGCAGTTCCCTGGGGAAGGCCCTGCTCTCCTGATAGCCATACGTTCAGTGTCCGATAAAAAGGAAGATGGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAATCTCTCCTTGCACATCAAAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATATTAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTAGTC	!!!!!!!!!!!!!,!,!00474,,,,22227766;;;62766622332.....9973335333133,,,,111155557623369;;:9986773329&lt;223366:...3933322223998&lt;444000&lt;&lt;&lt;&lt;&gt;&lt;&lt;&lt;?ABDD?????D;;;;DD???:::BBAAAABD:666FFFFFFDDFFFDDB8988A20//222&gt;&gt;&gt;=AAA&#64;BAA??==AAAAB==:;&lt;AA?88D==;;:::4F;7533??ABB5544&gt;&#64;&#64;&#64;&#64;&#64;?011==BBBBBDDFFFFFFFFFFFFCCCCCFFFFFFFFFFFFFFFFFDDDFDDDFDBAAA&gt;&gt;53310000226694445DFFFHIIIHHHIIIIIIIDFHFFDDDGGFF&lt;=666FHFFFHIIIIFFFFFFFF;;::FFF	AS:i:233	XS:i:218	XF:i:3	XE:i:4	XN:i:0
-</pre>
-
-The problem was that the V segment was completely digested in favor of the J segment.
-
-<pre>
-           351                                            400
-GWYEMNS10GHZUF CTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
-TRAJ16         ~~~~GCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
-TRAV14N-3      CTGTGCAGC...AAGTG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-           401                                            450
-GWYEMNS10GHZUF TAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTA
-TRAJ16         TAAAGGTGTACCTGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-TRAV14N-3      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-</pre>
-
-This triggered an infinite loop when calling `is.germline()`.
-
-[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
-
-Now the function should return as in the following example.
-
-<pre>
-yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
-## [1] "a.A14N3A16L9"
-</pre>
diff --git a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
deleted file mode 100644
index a4efb15..0000000
--- a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
+++ /dev/null
@@ -1,31 +0,0 @@
-Is it a bug in the software or a bug in the concept ?
-
-<pre>
-> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]
-[1] "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"
-[2] "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR"
-> V_after_C['TRAV14-1',]
-[1] "GCAGCAAGTG"
-> J_before_FGxG['TRAJ43',]
-[1] "GCAATAACAACAATGCCCCACGA"
-</pre>
-
-<pre>
-aAn.1A14-1A43L9
- A   A   A   N   N   N   A   P   R
-GCA GCA GCT AAC AAC AAT GCC CCA CGA
-GCA GCA agt g
-     gc aaT AAC AAC AAT GCC CCA CGA
-</pre>
-
-<pre>
-aAn.1A14-1A43L9
- A   A   N   N   N   N   A   P   R
-GCA GCT AAT AAC AAC AAT GCC CCA CGA
-GCA GCa agt g
-     gc AAT AAC AAC AAT GCC CCA CGA
-</pre>
-
-----
-
-This is a collision (different colonotypes giving the same Yassai ID) rather than a bug in the implementation → [[done]].
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
deleted file mode 100644
index c95cbe8..0000000
--- a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
+++ /dev/null
@@ -1,18 +0,0 @@
-The reason is the following bug in EMBOSS.
-
-<pre>
-echo -e '>A\nAAAAAA' > test-1.fa
-cat test-1.fa 
-# >A
-# AAAAAA
-seqret test-1.fa:A stdout
-# Read and write (return) sequences
-# >A
-# AAAAAA
-mkdir test
-seqret test-1.fa:A stdout
-# Read and write (return) sequences
-# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
-# Error: Unable to read sequence 'test-1.fa:A'
-# Died: seqret terminated: Bad value for '-sequence' and no prompt
-</pre>
diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
deleted file mode 100644
index 1648dce..0000000
--- a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
+++ /dev/null
@@ -1,13 +0,0 @@
-<pre>
-> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
-[1] "tg.integer(0)A2A61L13"
-</pre>
-
-[[Done]] in  `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
-
-Result after correction:
-
-<pre>
-> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
-[1] "tg.A2A61L13"
-</pre>
diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
deleted file mode 100644
index 95a3173..0000000
--- a/Bugs/Use_basename_case-insensitively.mdwn
+++ /dev/null
@@ -1,6 +0,0 @@
-Problem:
-
-    $ basename foo.fastq .fastq
-    foo
-    $ basename foo.FASTQ .fastq
-    foo.FASTQ
diff --git a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
deleted file mode 100644
index 3899e4e..0000000
--- a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
+++ /dev/null
@@ -1,18 +0,0 @@
-This would prevent horrors like:
-
-<pre>
-$ ../scripts/clonotypeR detect .fastq 
-[bam_header_read] EOF marker is absent. The input is probably truncated.
-[bsw2_aln] fail to open file '.fastq'. Abort!
-[samopen] SAM header is present: 169 sequences.
-[sam_read1] reference 'SN:TRDV5	LN:344
-3
-
-19
-
-3
-
-
-' is recognized as '*'.
-[main_samview] truncated file.
-</pre>
diff --git a/Bugs/done.mdwn b/Bugs/done.mdwn
deleted file mode 100644
index 0a666ab..0000000
--- a/Bugs/done.mdwn
+++ /dev/null

(Diff truncated)

diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index 3de0e56..32f4fe7 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -57,7 +57,7 @@ library(clonotypeR)
 
 The data is a table of 120 clonotypes in the `extdata` folder of the package.
 The command `read_clonotypes` will parse it in a data frame.  The clonotypes
-are arbitrarly assigned to three libraries called `A`, `B`, and `C`.  The
+are arbitrarily assigned to three libraries called `A`, `B`, and `C`.  The
 `read_clonotypes` comments determines at load time if the peptidic sequence has
 a stop codon or is frame-shifted, and records the information in the
 `unproductive` column.
@@ -78,7 +78,7 @@ head(clonotype_table(levels(clonotypes$lib), "J", data=clonotypes))
 ```
 
 ClonotypeR provides other functions for further analysis.  `yassai_identifier`
-calculates a unique indentifier using the `V`, `J`, peptidic and nucleotidic
+calculates a unique identifier using the `V`, `J`, peptidic and nucleotidic
 information, following the work of [Yassai et al](http://dx.doi.org/10.1007/s00251-009-0383-x).
 
 ```{r yassai_identifier}
@@ -100,7 +100,7 @@ common_clonotypes(data=clonotypes)
 ```
 
 With deeper data, a typical follow-up would be to identify differentially
-represnted clonotypes between libraries, for instance with the `edgeR` package,
+represented clonotypes between libraries, for instance with the `edgeR` package,
 or to calculate distance between libraries, for instance with the
 `vegan` package.
 
@@ -109,7 +109,7 @@ Example data (3 x 2,000 reads)
 ------------------------------
 
 The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
+is a sub-sample of three sequence libraries of mouse T cell receptors &alpha; (2,000
 reads each) made on the 454 Titanium or the 454 junior platforms.  The original
 libraries will be deposited in public databanks after publication in a
 peer-reviewed journal.
@@ -210,7 +210,7 @@ The command `summary(clonotypes)` already provides useful information.
 summary(clonotypes)
 ```
 
-Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarly named `abc`. 
+Identify unique clonotypes, count their sequences in the libraries `A`, `B` and `C`, and store the result as a table arbitrarily named `abc`. 
 
 ```{r explore_data2}
 abc <- clonotype_table(c('A','B','C'), data=clonotypes)

diff --git a/man/common_clonotypes.Rd b/man/common_clonotypes.Rd
index 3d239ca..9005ee0 100644
--- a/man/common_clonotypes.Rd
+++ b/man/common_clonotypes.Rd
@@ -29,7 +29,7 @@ quantitatively the overlap between each pair of libraries.
 \arguments{
   \item{group1}{A character vector containing clonotype library names.}
   \item{group2}{A character vector containing clonotype library names.}
-  \item{mode}{Only when producing a matrix of pairwise comparisions: \dQuote{count} (default) or \dQuote{abundance}, see below.}
+  \item{mode}{Only when producing a matrix of pairwise comparisons: \dQuote{count} (default) or \dQuote{abundance}, see below.}
   \item{data}{A clonotype table where the data is stored.}
 }
 

diff --git a/man/common_clonotypes.Rd b/man/common_clonotypes.Rd
index 3d239ca..9005ee0 100644
--- a/man/common_clonotypes.Rd
+++ b/man/common_clonotypes.Rd
@@ -29,7 +29,7 @@ quantitatively the overlap between each pair of libraries.
 \arguments{
   \item{group1}{A character vector containing clonotype library names.}
   \item{group2}{A character vector containing clonotype library names.}
-  \item{mode}{Only when producing a matrix of pairwise comparisions: \dQuote{count} (default) or \dQuote{abundance}, see below.}
+  \item{mode}{Only when producing a matrix of pairwise comparisons: \dQuote{count} (default) or \dQuote{abundance}, see below.}
   \item{data}{A clonotype table where the data is stored.}
 }
 

diff --git a/DESCRIPTION b/DESCRIPTION
index c73ec16..8e69f9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: High throughput analysis of T cell antigen receptor sequences
  The purpose of this package is to process and quantitatively analyse millions
  of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
 License: file LICENSE
-Depends: methods
+Imports: methods
 Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
 VignetteBuilder: knitr
 Packaged: 2013-12-11 10:22:39 UTC; charles
diff --git a/NAMESPACE b/NAMESPACE
index d75f824..2d083c2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,2 @@
+importFrom(methods, setMethod)
 exportPattern("^[[:alpha:]]+")

diff --git a/Bugs.mdwn b/Bugs.mdwn
new file mode 100644
index 0000000..1106591
--- /dev/null
+++ b/Bugs.mdwn
@@ -0,0 +1,12 @@
+If you've found a bug in clonotypeR, post about it here. [[TODO]] items go
+elsewhere. Link items to [[Bugs/done]] when done.
+
+The [[!shortcut name=commit url="http://source.clonotyper.branchable.com/?p=source.git;a=commitdiff;h=%s"]].
+You can use it to link to the commit that fixed the bug, as in `\[[!commit 7cf11805d84ff8dc6a537c17e73efa275077915d]]`.
+
+There are [[!pagecount pages="Bugs/* and !Bugs/done and !Bugs/discussion and 
+!link(patch) and !link(Bugs/done) and !Bugs/*/*"]] "open" bugs:
+
+[[!inline pages="Bugs/* and !Bugs/done and !Bugs/discussion and 
+!link(patch) and !link(Bugs/done) and !Bugs/*/*"
+actions=yes rootpage="Bugs" postformtext="Add a new bug titled:" show=0]]
diff --git a/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
new file mode 100644
index 0000000..7cdfc91
--- /dev/null
+++ b/Bugs/Clonotype_that_takes_ages_for_calculating_the_Yassai_identifier..mdwn
@@ -0,0 +1,55 @@
+Problem
+-------
+
+<pre>
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
+# takes ages
+
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAGCAACCGCAACTTCAAGTGGCCAGAAGCTGGTT", pep="AATATSSGQKLV"))
+## [1] "aTa.2A14N3A16L12"
+# returns immediately.
+</pre>
+
+
+Troubleshooting
+---------------
+
+The problematic clonotype comes from read `GWYEMNS10GHZUF`.
+
+<pre>
+&#64;GWYEMNS10GHZUF
+gactAACTGGTACACAGCAGGTTCTGGGTTCTGGATGTGCAGGTACACCTTTAATATGGTCCCCTGGCCAAAAACCAGCTTCTGGCCACTTGAAGTTGCACAGAAGTAGGTGGCTGAGTCTCCAGGCTGAGAGTCTTTGATGTGCAAGGAGAGATTTTTCTCCCTTTTATTGAAGAAGATTGTGAATCGTCCATCTTCCTTTTTATCGGACACTGAACGTATGGCTATCAGGAGAGCAGGGCCTTCCCCAGGGAACTGCTGGTACCATGGGAAGTAGTCAAAAGCACTGTTCTCAtaactagcagttcagaattgcggtctctccttccccagactgtcagagattggagtcgtgggagacaaggcacacaggggataggngngnnnnnnnnnnnnn
++
+FFF::;;FFFFFFFFIIIIHFFFHF666=&lt;FFGGDDDFFHFDIIIIIIIHHHIIIHFFFD54449662200001335&gt;&gt;AAABDFDDDFDDDFFFFFFFFFFFFFFFFFCCCCCFFFFFFFFFFFFDDBBBBB==110?&#64;&#64;&#64;&#64;&#64;&gt;4455BBA??3357;F4:::;;==D88?AA&lt;;:==BAAAA==??AAB&#64;AAA=&gt;&gt;&gt;222//02A8898BDDFFFDDFFFFFF666:DBAAAABB:::???DD;;;;D?????DDBA?&lt;&lt;&lt;&gt;&lt;&lt;&lt;&lt;000444&lt;8993222233393...:663322&lt;9233776899:;;963326755551111,,,,3313335333799.....23322666726;;;66772222,,,,47400!,!,!!!!!!!!!!!!!
+</pre>
+
+Here is the alignment made by clonotypeR
+
+<pre>
+GWYEMNS10GHZUF	16	TRAV14N-3	105	17	49S17M1I29M1I201M99S	*	0	0	NNNNNNNNNNNNNCNCNCCTATCCCCTGTGTGCCTTGTCTCCCACGACTCCAATCTCTGACAGTCTGGGGAAGGAGAGACCGCAATTCTGAACTGCTAGTTATGAGAACAGTGCTTTTGACTACTTCCCATGGTACCAGCAGTTCCCTGGGGAAGGCCCTGCTCTCCTGATAGCCATACGTTCAGTGTCCGATAAAAAGGAAGATGGACGATTCACAATCTTCTTCAATAAAAGGGAGAAAAATCTCTCCTTGCACATCAAAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATATTAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTAGTC	!!!!!!!!!!!!!,!,!00474,,,,22227766;;;62766622332.....9973335333133,,,,111155557623369;;:9986773329&lt;223366:...3933322223998&lt;444000&lt;&lt;&lt;&lt;&gt;&lt;&lt;&lt;?ABDD?????D;;;;DD???:::BBAAAABD:666FFFFFFDDFFFDDB8988A20//222&gt;&gt;&gt;=AAA&#64;BAA??==AAAAB==:;&lt;AA?88D==;;:::4F;7533??ABB5544&gt;&#64;&#64;&#64;&#64;&#64;?011==BBBBBDDFFFFFFFFFFFFCCCCCFFFFFFFFFFFFFFFFFDDDFDDDFDBAAA&gt;&gt;53310000226694445DFFFHIIIHHHIIIIIIIDFHFFDDDGGFF&lt;=666FHFFFHIIIIFFFFFFFF;;::FFF	AS:i:233	XS:i:218	XF:i:3	XE:i:4	XN:i:0
+</pre>
+
+The problem was that the V segment was completely digested in favor of the J segment.
+
+<pre>
+           351                                            400
+GWYEMNS10GHZUF CTGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
+TRAJ16         ~~~~GCAACTTCAAGTGGCCAGAAGCTGGTTTTTGGCCAGGGGACCATAT
+TRAV14N-3      CTGTGCAGC...AAGTG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+           401                                            450
+GWYEMNS10GHZUF TAAAGGTGTACCTGCACATCCAGAACCCAGAACCTGCTGTGTACCAGTTA
+TRAJ16         TAAAGGTGTACCTGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+TRAV14N-3      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+</pre>
+
+This triggered an infinite loop when calling `is.germline()`.
+
+[[Done]] in `42ab98729c5c77462b5929b00ee973074ae4c1c7`.
+
+Now the function should return as in the following example.
+
+<pre>
+yassai_identifier(c(V="TRAV14N-3", J="TRAJ16", dna="GCAACTTCAAGTGGCCAGAAGCTGGTT", pep="ATSSGQKLV"))
+## [1] "a.A14N3A16L9"
+</pre>
diff --git a/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
new file mode 100644
index 0000000..a4efb15
--- /dev/null
+++ b/Bugs/Different_clonotypes_give_the_same_Yassai_identifier..mdwn
@@ -0,0 +1,31 @@
+Is it a bug in the software or a bug in the concept ?
+
+<pre>
+> rownames(dd)[grep('aAn.1A14-1A43L9', dd.yassai)]
+[1] "TRAV14-1 TRAJ43 GCAGCAGCTAACAACAATGCCCCACGA AAANNNAPR"
+[2] "TRAV14-1 TRAJ43 GCAGCTAATAACAACAATGCCCCACGA AANNNNAPR"
+> V_after_C['TRAV14-1',]
+[1] "GCAGCAAGTG"
+> J_before_FGxG['TRAJ43',]
+[1] "GCAATAACAACAATGCCCCACGA"
+</pre>
+
+<pre>
+aAn.1A14-1A43L9
+ A   A   A   N   N   N   A   P   R
+GCA GCA GCT AAC AAC AAT GCC CCA CGA
+GCA GCA agt g
+     gc aaT AAC AAC AAT GCC CCA CGA
+</pre>
+
+<pre>
+aAn.1A14-1A43L9
+ A   A   N   N   N   N   A   P   R
+GCA GCT AAT AAC AAC AAT GCC CCA CGA
+GCA GCa agt g
+     gc AAT AAC AAC AAT GCC CCA CGA
+</pre>
+
+----
+
+This is a collision (different colonotypes giving the same Yassai ID) rather than a bug in the implementation → [[done]].
diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
new file mode 100644
index 0000000..c95cbe8
--- /dev/null
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -0,0 +1,18 @@
+The reason is the following bug in EMBOSS.
+
+<pre>
+echo -e '>A\nAAAAAA' > test-1.fa
+cat test-1.fa 
+# >A
+# AAAAAA
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# >A
+# AAAAAA
+mkdir test
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
+# Error: Unable to read sequence 'test-1.fa:A'
+# Died: seqret terminated: Bad value for '-sequence' and no prompt
+</pre>
diff --git a/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
new file mode 100644
index 0000000..1648dce
--- /dev/null
+++ b/Bugs/Incorrect_identifiers_when_V-J_boundary_is_a_codon_boundary_.mdwn
@@ -0,0 +1,13 @@
+<pre>
+> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
+[1] "tg.integer(0)A2A61L13"
+</pre>
+
+[[Done]] in  `2b8514d18f312f627255b0f2eb0ec1bf4ffa48dd`, by return an empty chain instead of `integer(0)` when receiving an empty chain.
+
+Result after correction:
+
+<pre>
+> yassai_identifier(c(V='TRAV2', J='TRAJ61', dna='ATTGTGACTGACACAGGTACAGAATTAATAGGAAATTGGCA', pep='IVTDTGTELIGNW'))
+[1] "tg.A2A61L13"
+</pre>
diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
new file mode 100644
index 0000000..95a3173
--- /dev/null
+++ b/Bugs/Use_basename_case-insensitively.mdwn
@@ -0,0 +1,6 @@
+Problem:
+
+    $ basename foo.fastq .fastq
+    foo
+    $ basename foo.FASTQ .fastq
+    foo.FASTQ
diff --git a/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
new file mode 100644
index 0000000..3899e4e
--- /dev/null
+++ b/Bugs/clonotypeR_detect_should_test_the_existence_of_the_FASTQ_file..mdwn
@@ -0,0 +1,18 @@
+This would prevent horrors like:
+
+<pre>
+$ ../scripts/clonotypeR detect .fastq 
+[bam_header_read] EOF marker is absent. The input is probably truncated.
+[bsw2_aln] fail to open file '.fastq'. Abort!
+[samopen] SAM header is present: 169 sequences.
+[sam_read1] reference 'SN:TRDV5	LN:344
+3
+
+19
+
+3
+
+
+' is recognized as '*'.
+[main_samview] truncated file.
+</pre>
diff --git a/Bugs/done.mdwn b/Bugs/done.mdwn
new file mode 100644
index 0000000..0a666ab
--- /dev/null
+++ b/Bugs/done.mdwn

(Diff truncated)

diff --git a/DESCRIPTION b/DESCRIPTION
index c73ec16..8e69f9b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: High throughput analysis of T cell antigen receptor sequences
  The purpose of this package is to process and quantitatively analyse millions
  of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
 License: file LICENSE
-Depends: methods
+Imports: methods
 Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
 VignetteBuilder: knitr
 Packaged: 2013-12-11 10:22:39 UTC; charles
diff --git a/NAMESPACE b/NAMESPACE
index d75f824..2d083c2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,2 @@
+importFrom(methods, setMethod)
 exportPattern("^[[:alpha:]]+")

diff --git a/DESCRIPTION b/DESCRIPTION
index a0daca5..c73ec16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.6
+Version: 1.3.1
 Date: 2014-04-08
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index f121ece..3de0e56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -39,7 +39,7 @@ examples are available on line at
 
 *This example analysis assumes a
 [unix](https://en.wikipedia.org/wiki/Operating%5Fsystem%23UNIX%5Fand%5FUNIX%2Dlike%5Foperating%5Fsystems)
-system (Linux, Mac OS, …)*
+system (Linux, Mac OS, ...)*
 
 
 Test data
@@ -105,11 +105,11 @@ or to calculate distance between libraries, for instance with the
 `vegan` package.
 
 
-Example data (3 × 2,000 reads)
+Example data (3 x 2,000 reads)
 ------------------------------
 
 The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors α (2,000
+is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
 reads each) made on the 454 Titanium or the 454 junior platforms.  The original
 libraries will be deposited in public databanks after publication in a
 peer-reviewed journal.

diff --git a/index.mdwn b/index.mdwn
index 7a89d51..357e7b9 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -45,6 +45,8 @@ to try alternative solutions, you can have a look at
 
 ### Recent news
 
+ * March 2014: New stable version [1.2](http://www.bioconductor.org/packages/2.14/bioc/html/clonotypeR.html)
+   released on Bioconductor.
  * 11 December 2013: Version 1.1.3 adding a `long` option to `yassai_identifier`, solving
    the problem of ID collisions.
  * 23 October 2013: Version 1.1.2 adding a new option to `clonotype_table` for randomly

diff --git a/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
new file mode 100644
index 0000000..c95cbe8
--- /dev/null
+++ b/Bugs/Does_not_work_with_EMBOSS_6.6.0..mdwn
@@ -0,0 +1,18 @@
+The reason is the following bug in EMBOSS.
+
+<pre>
+echo -e '>A\nAAAAAA' > test-1.fa
+cat test-1.fa 
+# >A
+# AAAAAA
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# >A
+# AAAAAA
+mkdir test
+seqret test-1.fa:A stdout
+# Read and write (return) sequences
+# Error: Query 'test-1.fa:A' query field '1.fa' not defined for datatype 'sequence'
+# Error: Unable to read sequence 'test-1.fa:A'
+# Died: seqret terminated: Bad value for '-sequence' and no prompt
+</pre>

diff --git a/Bugs/Use_basename_case-insensitively.mdwn b/Bugs/Use_basename_case-insensitively.mdwn
new file mode 100644
index 0000000..95a3173
--- /dev/null
+++ b/Bugs/Use_basename_case-insensitively.mdwn
@@ -0,0 +1,6 @@
+Problem:
+
+    $ basename foo.fastq .fastq
+    foo
+    $ basename foo.FASTQ .fastq
+    foo.FASTQ

diff --git a/DESCRIPTION b/DESCRIPTION
index 1309b59..c73ec16 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.3.0
+Version: 1.3.1
 Date: 2014-04-08
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
diff --git a/vignettes/clonotypeR.Rmd b/vignettes/clonotypeR.Rmd
index f121ece..3de0e56 100644
--- a/vignettes/clonotypeR.Rmd
+++ b/vignettes/clonotypeR.Rmd
@@ -39,7 +39,7 @@ examples are available on line at
 
 *This example analysis assumes a
 [unix](https://en.wikipedia.org/wiki/Operating%5Fsystem%23UNIX%5Fand%5FUNIX%2Dlike%5Foperating%5Fsystems)
-system (Linux, Mac OS, …)*
+system (Linux, Mac OS, ...)*
 
 
 Test data
@@ -105,11 +105,11 @@ or to calculate distance between libraries, for instance with the
 `vegan` package.
 
 
-Example data (3 × 2,000 reads)
+Example data (3 x 2,000 reads)
 ------------------------------
 
 The data provided on-line at <http://clonotyper.branchable.com/example_data/>
-is a sub-sample of three sequence librairies of mouse T cell receptors α (2,000
+is a sub-sample of three sequence librairies of mouse T cell receptors &alpha; (2,000
 reads each) made on the 454 Titanium or the 454 junior platforms.  The original
 libraries will be deposited in public databanks after publication in a
 peer-reviewed journal.

diff --git a/DESCRIPTION b/DESCRIPTION
index 1b4302b..1309b59 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.2.0
+Version: 1.3.0
 Date: 2014-04-08
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/DESCRIPTION b/DESCRIPTION
index a0daca5..1b4302b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.6
+Version: 1.2.0
 Date: 2014-04-08
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>

diff --git a/ChangeLog b/ChangeLog
index 96b84e2..8c90a52 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -11,7 +11,7 @@
 	* Change biocviews to “Sequencing”,
 
 2013-12-11  Charles Plessy <plessy@riken>
-	* Commited 1.1.3 to Bioconductor.
+	* Committed 1.1.3 to Bioconductor.
 	* Fixed two bugs in yassai_identifier().
 	  - Infinite loop when the CDR3 is fully contained in the J segment.
 	  - Bogus 'integer(0)' output when there are only germline residues.

diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..96b84e2
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,80 @@
+2014-04-08  Charles Plessy <plessy@riken.jp>
+	* Version 1.1.6
+	* Transfer “NEWS” to ChangeLog and add release notes to “NEWS”.
+
+2014-04-03  Charles Plessy <plessy@riken.jp>
+	* Version 1.1.5
+	* Mention the GitHub bridge in the documentation
+
+2014-03-05  Bioc admins
+	* Version 1.1.4.
+	* Change biocviews to “Sequencing”,
+
+2013-12-11  Charles Plessy <plessy@riken>
+	* Commited 1.1.3 to Bioconductor.
+	* Fixed two bugs in yassai_identifier().
+	  - Infinite loop when the CDR3 is fully contained in the J segment.
+	  - Bogus 'integer(0)' output when there are only germline residues.
+	* Avoid more collisions by indicating the position of the V-J junction
+	  when there is no codon ID to indicate.
+	* Mark and filter out clonotypes with ambiguous ('N') nucleotides.
+
+2013-12-05  Charles Plessy <plessy@riken>
+	* New "long" option to yassai_identifier(), to avoid collisions.
+
+2013-11-19  Charles Plessy <plessy@riken.jp>
+	* New references from NCBI, updating TRDV5.
+
+2013-10-23  Charles Plessy <plessy@riken.jp>
+	* Commited 1.1.2 to Bioconductor.
+	* clonotype_table: new option to randomly "sample" libraries.
+
+2013-10-17  Charles Plessy <plessy@riken.jp>
+	* Commited 1.1.1 to Bioconductor.
+	* common_clonotypes: new mode to calculate the "abundance" relatively
+	  to one library.
+
+2013-10-07  Charles Plessy <plessy@riken.jp>
+	* Commited 0.99.6 to Bioconductor.
+	* Added unit tests for yassai_identifier(). 
+
+2013-08-01  Charles Plessy <plessy@riken.jp>
+	* Unified the syntax of common_clonotypes and unique_clonotypes.
+
+2013-05-07  Charles Plessy <plessy@riken.jp>
+	* Resubmitted 0.99.5 to Bioconductor.
+	* Distribute a copy of the clonotypes extracted from example_data.
+	* Execute all examples in the vignette.
+
+2013-05-01  Charles Plessy <plessy@riken.jp>
+
+	* Resubmitted 0.99.4 to Bioconductor
+	* Moved the Markdown vignette to '/vignettes'.
+	* Added executable example with test data to the vignette.
+
+2013-04-26  Charles Plessy <plessy@riken.jp>
+
+	* Resubmitted 0.99.3 to Bioconductor
+	* Moved extra data to 'inst/extdata'.
+	* Moved the Markdown vignette to 'inst/vignettes'.
+
+2013-04-15  Charles Plessy <plessy@riken.jp>
+
+	* Resubmission after correcting yassai_identifier() and other warnings.
+
+2013-01-08  Charles Plessy <plessy@riken.jp>
+
+	* Leaner Bioconductor package, without the wiki documentation.
+
+2012-.....  Charles Plessy <plessy@riken.jp>
+
+	* Many entries missing.
+
+2012-10-10  Charles Plessy <plessy@riken.jp>
+
+	* Corrected Frenglish “improductive” with “unproductive”. 
+	  This can break backwards compatibility.
+
+2012-09-06  Charles Plessy <plessy@riken.jp>
+
+	* Initial release
diff --git a/DESCRIPTION b/DESCRIPTION
index ee152f8..a0daca5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,21 +1,19 @@
 Package: clonotypeR
 Type: Package
 Title: High throughput analysis of T cell antigen receptor sequences
-Version: 1.1.4
-Date: 2013-12-11
+Version: 1.1.6
+Date: 2014-04-08
 Author: Charles Plessy <plessy@riken.jp>
 Maintainer: Charles Plessy <plessy@riken.jp>
-Description: High throughput analysis of T cell antigen receptor
-        sequences The genes encoding T cell receptors are created by
-        somatic recombination, generating an immense combination of V,
-        (D) and J segments.  Additional processes during the
-        recombination create extra sequence diversity between the V an
-        J segments.  Collectively, this hyper-variable region is called
-        the CDR3 loop.
+Description: High throughput analysis of T cell antigen receptor sequences
+ The genes encoding T cell receptors are created by somatic recombination,
+ generating an immense combination of V, (D) and J segments.  Additional
+ processes during the recombination create extra sequence diversity between the
+ V an J segments.  Collectively, this hyper-variable region is called the CDR3
+ loop.
  .
- The purpose of this package is to process and quantitatively analyse
-        millions of V-CDR3-J combination, called clonotypes, from
-        multiple sequence libraries.
+ The purpose of this package is to process and quantitatively analyse millions
+ of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.
 License: file LICENSE
 Depends: methods
 Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
diff --git a/NEWS b/NEWS
index f3e6131..e8067a7 100644
--- a/NEWS
+++ b/NEWS
@@ -1,76 +1,28 @@
-2014-04-03  Charles Plessy <plessy@riken.jp>
-	* Version 1.1.5
-	* Mention the GitHub bridge in the documentation
+Changes in version 1.2.0
 
-2014-03-05  Bioc admins
-	* Version 1.1.4.
-	* Change biocviews to “Sequencing”,
+NEW FEATURES
 
-2013-12-11  Charles Plessy <plessy@riken>
-	* Commited 1.1.3 to Bioconductor.
-	* Fixed two bugs in yassai_identifier().
-	  - Infinite loop when the CDR3 is fully contained in the J segment.
-	  - Bogus 'integer(0)' output when there are only germline residues.
-	* Avoid more collisions by indicating the position of the V-J junction
-	  when there is no codon ID to indicate.
-	* Mark and filter out clonotypes with ambiguous ('N') nucleotides.
+    o   Added a “long” option to yassai_identifier(), where every amino acid is
+        represented.  This solves the problem of ID collisions, where a single
+        identifier could be produced by two different clonotypes.
 
-2013-12-05  Charles Plessy <plessy@riken>
-	* New "long" option to yassai_identifier(), to avoid collisions.
+    o   Added a new option to clonotype_table() for randomly sampling libraries.
 
-2013-11-19  Charles Plessy <plessy@riken.jp>
-	* New references from NCBI, updating TRDV5.
+    o   Added a new mode to common_clonotypes() for calculating the abundance
+        relatively to one library.
 
-2013-10-23  Charles Plessy <plessy@riken.jp>
-	* Commited 1.1.2 to Bioconductor.
-	* clonotype_table: new option to randomly "sample" libraries.
+    o   Unified the syntax of common_clonotypes() and unique_clonotypes().
 
-2013-10-17  Charles Plessy <plessy@riken.jp>
-	* Commited 1.1.1 to Bioconductor.
-	* common_clonotypes: new mode to calculate the "abundance" relatively
-	  to one library.
+BUG FIXES
 
-2013-10-07  Charles Plessy <plessy@riken.jp>
-	* Commited 0.99.6 to Bioconductor.
-	* Added unit tests for yassai_identifier(). 
+    o   Removed infinite loop in yassai_identifier() when the germinal V
+        sequence was completely absent from the CDR3.
 
-2013-08-01  Charles Plessy <plessy@riken.jp>
-	* Unified the syntax of common_clonotypes and unique_clonotypes.
+    o   Corrected output bug where “integer(0)” was returned if the V–J
+        boundary was a codon boundary.
 
-2013-05-07  Charles Plessy <plessy@riken.jp>
-	* Resubmitted 0.99.5 to Bioconductor.
-	* Distribute a copy of the clonotypes extracted from example_data.
-	* Execute all examples in the vignette.
+    o   yassai_identifier(): properly encode the names of the V and J segments.
 
-2013-05-01  Charles Plessy <plessy@riken.jp>
+Changes in version 1.0.0
 
-	* Resubmitted 0.99.4 to Bioconductor
-	* Moved the Markdown vignette to '/vignettes'.
-	* Added executable example with test data to the vignette.
-
-2013-04-26  Charles Plessy <plessy@riken.jp>
-
-	* Resubmitted 0.99.3 to Bioconductor
-	* Moved extra data to 'inst/extdata'.
-	* Moved the Markdown vignette to 'inst/vignettes'.
-
-2013-04-15  Charles Plessy <plessy@riken.jp>

(Diff truncated)