[Seqinr-commits] r1606 - pkg/inst/doc/src/appendix

[noreply at r-forge.r-project.org]

Author: lobry
Date: 2009-04-26 20:16:29 +0200 (Sun, 26 Apr 2009)
New Revision: 1606

Modified:
   pkg/inst/doc/src/appendix/releasenotes.rnw
Log:
new kaks behaviour

Modified: pkg/inst/doc/src/appendix/releasenotes.rnw
===================================================================
--- pkg/inst/doc/src/appendix/releasenotes.rnw	2009-04-26 11:56:02 UTC (rev 1605)
+++ pkg/inst/doc/src/appendix/releasenotes.rnw	2009-04-26 18:16:29 UTC (rev 1606)
@@ -23,9 +23,14 @@
 \item As pointed out on the seqinr diffusion list on 23-APR-2009
 by Darren Obbard there was an obscure error message when function
 \texttt{kaks()} was called with an alignment such that the number
-of nucleotides was not a multiple of 3 after gap removal. The error 
-message is now more explicit. Documentation of the function has 
-been clarified accordingly.
+of nucleotides was not a multiple of 3 after gap removal. This check
+was partial as an alignment with out-of-frame gaps but with
+a total number of gaps multiple of 3 was not detected.
+The new behaviour is that if at least one non ACGT base is found in a
+codon, then the whole codon is forced to a gap codon (\texttt{---}).
+The documentation of the function has been clarified accordingly,
+and a new alignment file \texttt{DarrenObbard.fasta} added in
+the \texttt{sequences} folder to check this new behaviour.
 
 \item Function \texttt{readBins()} is now more tolerant when there
 is an extra column with possibly empty fields in data by forcing