[Seqinr-forum] release 2.0-3

[Jean lobry]

Dear seqinR,

seqinr 2.0-3 is on its way to CRAN. My advice is to update
if you are using one of the functions named thereafter, otherwise
there is no hurry (in theory seqinr is backward compatible up
to R version 2.5.0 in the past).

Best,

Z.

Release Notes for version 2.0-3
-------------------------------


  o As pointed out on the seqinr diffusion list on 23-APR-2009
    by Darren Obbard there was an obscure error message when function
    kaks() was called with an alignment such that the number
    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 (---).
    The documentation of the function has been clarified accordingly,
    and a new alignment file DarrenObbard.fasta added in
    the sequences folder to check this new behaviour.

  o Function readBins() is now more tolerant when there
    is an extra column with possibly empty fields in data by forcing
    the fill argument of read.table() function to TRUE.

  o As pointed out by e-mail on 30-MAR-2009 by Yann Lesecque there
    was a bug in the getTrans() function: when applied to a
    list of sequences with all the same length the returned result
    was a matrix instead of a list. This is now fixed.

  o New utility functions readPanels() and readBins() to import
    data from GeneMapper configuration files. Four example files
    are now in the abif folder.

  o Function peakabif() now returns the heights and surfaces of peaks
    in addition to their location.

  o New utility function al2bp() to convert a forensic microsatellite
    allele name into its length in base pairs. Conventions used to name
    forensic microsatellite alleles (STR) are described
    in Bar et al. (1994). The name 9.3 means for instance that there are
    9 repetitions of the complete base oligomer and an incomplete
    repeat with 3 bp.

-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/