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bp_pairwise_kaks(1p) [debian man page]

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

NAME

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

SYNOPSIS

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

DESCRIPTION

	 This script will take as input a dataset of cDNA sequences verify
	that they contain no stop codons, align them in protein space,
	project the alignment back into cDNA and estimate the Ka
	(non-synonymous) and Ks (synonymous) substitutions based on the ML
	method of Yang with the PAML package.

	Requires:
	* bioperl-run package
	* PAML program codeml or yn00
	* Multiple sequence alignment programs Clustalw OR T-Coffee

	Often there are specific specific parameters you want to run when you
	a computing Ka/Ks ratios so consider this script a starting point and
	do not rely it on for every situation.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

	Jason Stajich jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						      BP_PAIRWISE_KAKS(1p)

Check Out this Related Man Page

BP_AACOMP(1p)						User Contributed Perl Documentation					     BP_AACOMP(1p)

NAME

       aacomp - amino acid composition of protein sequences

SYNOPSIS

	 aacomp [-f/--format FORMAT] [-h/--help] filename
	 or
	 aacomp [-f/--format FORMAT] < filename
	 or
	 aacomp [-f/--format FORMAT] -i filename

DESCRIPTION

       This scripts prints out the count of amino acids over all protein sequences from the input file.

OPTIONS

       The default sequence format is fasta.

       The sequence input can be provided using any of the three methods:

       unnamed argument
	    aacomp filename

       named argument
	    aacomp -i filename

       standard input
	    aacomp < filename

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

HISTORY

       Based on aacomp.c from an old version of EMBOSS

perl v5.14.2							    2012-03-02							     BP_AACOMP(1p)
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