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PhyloSim specifications

Information


Unique identifier OMICS_15371
Name PhyloSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0.2
Stability Stable
Requirements
R.oo, ape, compoisson, ggplot2
Source code URL https://cran.r-project.org/src/contrib/phylosim_3.0.2.tar.gz
Maintained Yes

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Maintainer


  • person_outline Botond Sipos <>

Publication for PhyloSim

PhyloSim in publications

 (3)
PMCID: 5410925
PMID: 27616324
DOI: 10.1093/sysbio/syw066

[…] substitution models and their parameter values using the r-package phangorn () on the empirical data sets and applied these when simulating sequences on the simulated tree using the r-package phylosim () simulated alignments that were invariable were removed from the data set. basic properties of the simulated tree set of alignments are similar to the actual data (). replication […]

PMCID: 4462595
PMID: 26020646
DOI: 10.1371/journal.pcbi.1004095

[…] assessment of their respective performances and thus help the biologist in choosing objectively proper tools []., standard tools to simulate sequence evolution along trees such as indelible [] or phylosim [] can be adapted to simulate hgt. hgt events cause the relevant gene trees to conflict with the species tree. such hgt events can be simulated through subtree pruning and regrafting […]

PMCID: 3364941
PMID: 22693434
DOI: 10.1371/journal.pcbi.1002495

[…] dependency among sites., the rate of variation among sites can be introduced from the user., amino acid models implemented in alf: pam, jtt, wag, lg, customp, gcb., amino acid models implemented in phylosim: cprev, jtt, jtt (dcmut), lg, mtart, mtmam, mtrev24, mtzoa, wag., when attempting to simulate a complex evolutionary scenario, several programs developed under the forward-time approach may […]


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PhyloSim institution(s)
EMBL-European Bioinformatics Institute, Hinxton, UK; Laboratory of Molecular Biodiversity, Institute of Genetics, Biological Research Center, Szeged, Hungary
PhyloSim funding source(s)
This work was supported by an EMBO short-term fellowship and an EMBL Interdisciplinary Postdoc (EIPOD) under Marie Curie Actions (COFUND), and a Gates Cambridge Scholarship and is a member of Darwin College, University of Cambridge.

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