1BP_PAIRWISE_KAKS(1)   User Contributed Perl Documentation  BP_PAIRWISE_KAKS(1)
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NAME

6       pairwise_kaks - script to calculate pairwise Ka,Ks for a set of
7       sequences
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SYNOPSIS

10       pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f
11       fasta/genbank/embl...] [-msa tcoffee/clustal] [-kaks yn00/codeml]
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DESCRIPTION

14         This script will take as input a dataset of cDNA sequences verify
15        that they contain no stop codons, align them in protein space,
16        project the alignment back into cDNA and estimate the Ka
17        (non-synonymous) and Ks (synonymous) substitutions based on the ML
18        method of Yang with the PAML package.
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20        Requires:
21        * bioperl-run package
22        * PAML program codeml or yn00
23        * Multiple sequence alignment programs Clustalw OR T-Coffee
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25        Often there are specific specific parameters you want to run when you
26        a computing Ka/Ks ratios so consider this script a starting point and
27        do not rely it on for every situation.
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FEEDBACK

30   Mailing Lists
31       User feedback is an integral part of the evolution of this and other
32       Bioperl modules. Send your comments and suggestions preferably to the
33       Bioperl mailing list.  Your participation is much appreciated.
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35         bioperl-l@bioperl.org                  - General discussion
36         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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38   Reporting Bugs
39       Report bugs to the Bioperl bug tracking system to help us keep track of
40       the bugs and their resolution. Bug reports can be submitted via the
41       web:
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43         http://bugzilla.open-bio.org/
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AUTHOR

46        Jason Stajich jason-at-bioperl-dot-org
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50perl v5.12.0                      2010-04-29               BP_PAIRWISE_KAKS(1)
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