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Pyvolve specifications

Information


Unique identifier OMICS_12252
Name Pyvolve
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Requirements
BioPython, SciPy, NumPy
Source code URL https://codeload.github.com/sjspielman/pyvolve/zip/master
Maintained Yes

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Maintainer


  • person_outline Stephanie J. Spielman <>

Publication for Pyvolve

Pyvolve in publications

 (5)
PMCID: 5804317
PMID: 29423346
DOI: 10.7717/peerj.4339

[…] number used the same model parameterizations for all three trees, i.e., replicate 1 employed the same model for 25, 50, and 100 taxa. simulations were conducted using the python simulation library pyvolve ()., we then inferred relative evolutionary rates in leisr in two modes: turning off rate heterogeneity during branch length optimization (“leisr”), and specifying a four-category discrete […]

PMCID: 5850840
PMID: 28957508
DOI: 10.1093/molbev/msx200

[…] length, ten random trees were computed to evaluate reproducibility. sequences of one million nucleotides were produced for each simulated genome in the phylogenies in the form of an alignment, using pyvolve ()., the three branch lengths we examined were chosen to model bacterial populations of within-species genomes (0.001), within-genera genomes (0.005), and interspecies genomes (0.01). […]

PMCID: 5452972
PMID: 28584717
DOI: 10.7717/peerj.3391

[…] a set of balanced, binary trees with different branch lengths and numbers of taxa, using the r package ape (). we then simulated sequence evolution along these trees using the python library pyvolve ()., we generated a total of 40 trees, using all pairwise combinations of five different branch lengths and eight different numbers of taxa. the branch lengths we used were 0.0025, 0.01, […]

PMCID: 5189966
PMID: 27959955
DOI: 10.1371/journal.ppat.1006114

[…] constraints in env, we simulated evolution along the phylogenetic tree in under the assumption that the experimentally measured preferences exactly match natural selection. specifically, we used pyvolve [] to simulate evolution using the experimentally informed site-specific codon substitution models described in [], which define mutation-fixation probabilities in terms of the amino-acid […]

PMCID: 4880944
PMID: 27230264
DOI: 10.1186/s12862-016-0688-y

[…] uced models, we used a mean of 10−3 substitutions/site/year and a standard deviation of 10 % of the mean for the ucln (note that in the uced, the mean equals the standard deviation). we then used pyvolve [] to simulate the evolution of sequences of length 5,000, 10,000, and 15,000 nt under the jukes-cantor substitution model., we compared all three clock models using the cross-validation […]


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Pyvolve institution(s)
Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
Pyvolve funding source(s)
This work was supported by National Institutes of Health, Grant No. F31GM113622; Army Research Office, Grant No. W911NF-12-1-0390; Defense Threat Reduction Agency, Grant No. HDTRA1-12-C-0007; and National Science Foundation, Cooperative Agreement No. DBI-0939454, BEACON Center.

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