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Enables phylogenetic analyses using deep mutational scanning data to inform the substitution models. Phydms uses the Experimentally Informed Codon Models (EICM) which describes the evolution of protein-coding genes in terms of their site-specific amino-acid preferences and allows to detect sites biologically interesting selection.

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phydms versioning

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phydms classification

phydms specifications

Software type:
Package/Module
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:
2.0.5
Requirements:
Pip, Bio++
Maintained:
Yes
Issue URL:
https://github.com/jbloomlab/phydms/issues

phydms support

Documentation

Maintainer

  • J. D. Bloom <>

Credits

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Publications

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).

Link to literature

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