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phydms specifications


Unique identifier OMICS_13094
Name phydms
Alternative name Phylogenetic analyses using Deep Mutational Scanning
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FATSQ, TXT
Output format TEX, LOG, TXT
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.5
Stability Stable
Pip, Bio++
Maintained Yes




No version available



  • person_outline J. D. Bloom

Publications for Phylogenetic analyses using Deep Mutational Scanning

phydms citations


Mapping mutational effects along the evolutionary landscape of HIV envelope

PMCID: 5910023
PMID: 29590010
DOI: 10.7554/eLife.34420.047

[…] legend to that figure. An algorithmic description of how the alignment and tree were generated are in and .For fitting of the phylogenetic substitution models, we used (,, version 2.2.1) to optimize the substitution model parameters and branch lengths on the fixed tree topology intree. The Goldman-Yang (or YNGKP) model used in is the M5 variant described by ), […]


A framework for exhaustively mapping functional missense variants

Mol Syst Biol
PMCID: 5740498
PMID: 29269382
DOI: 10.15252/msb.20177908

[…] We used the phydms software package (Bloom, ) to test three different models relating the effect of complementation‐enhancing substitutions in SUMO1 and UBE2I to actual preference for the substituted amino acid i […]


Accurate Measurement of the Effects of All Amino Acid Mutations on Influenza Hemagglutinin

PMCID: 4926175
PMID: 27271655
DOI: 10.3390/v8060155

[…] We sub-sampled human and swine H1 sequences (1 sequence per host per year) from the set of sequences from [], removed identical sequences, and built a sequence alignment. We then used phydms version 1.1.0 [] (, which in turn uses Bio++ [] for the likelihood calculations, to compare experimentally informed codon substitution models and other non-si […]

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phydms institution(s)
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
phydms 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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