01 Jul 2018 12:36:38 UTC
- Distribution: Bio-Tools-Phylo-PAML
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- Latest versionCDRAUG Carnë Draugand 2 contributors
- Aaron J Mackey
- Jason Stajich
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bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences
bp_pairwise_kaks.PLS -i INPUT-cDNA [-f FORMAT] [-o OUTPUT] \ [--msa tcoffee|clustal] [--kaks yn00|codeml]
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 Maximum Likelihood method of Yang with the PAML package.
Often there are specific specific parameters you want to run when you are computing Ka/Ks ratios so consider this script a starting point and do not rely it on for every situation.
- -i, --input
The input file with the cDNA sequences. Must have at least two sequences, and be in a format that Bio::SeqIO is capable to read. In addition, if Bio::SeqIO is inable to automatically identify the format, the -f option should be specified.
Technically not an option, this is a required value.
- -f, --format
Specify the format of INPUT-cDNA for Bio::SeqIO.
- -o, --output
Specify the file for output. Defaults to STDOUT.
Program used for alignment, either clustalw or tcoffee. Defaults to clustalw.
Program used for the Ka/Ks estimation, either codeml or yn00. Defaults to codeml.
- -v, --verbose
- -h, --help
Print help text.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/Support.html - About the mailing lists
Please direct usage questions or support issues to the mailing list: email@example.com
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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:
Jason Stajich <firstname.lastname@example.org>
This software is copyright (c) by Jason Stajich <email@example.com>.
This software is available under the same terms as the perl 5 programming language system itself.
Module Install Instructions
To install Bio::Tools::Phylo::PAML, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell install Bio::Tools::Phylo::PAML
For more information on module installation, please visit the detailed CPAN module installation guide.