This package uses a null model based on high-throughput measurements of a gene’s site-specific amino-acid preferences to detect sites of positive selection. phydms can use Experimentally Informed Codon Models (EICM) to describe the evolution of protein-coding genes for phylogenetic inference and the detection of biologically interesting selection.

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phydms classification

phydms specifications

Software type:
Package
Restrictions to use:
None
Output format:
TEX, LOG, TXT
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input format:
FASTA, FATSQ, TXT
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 3.0
Version:
1.3.0
Requirements:
Python v. 2.6+, Pip, Bio++

Publications

  • (Bloom, 2016) Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. bioRxiv.
    DOI: 10.1101/037689

phydms support

Documentation

Maintainer

Credits

Institution(s)

Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Funding source(s)

This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (grant R01 GM102198).

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