EvolSimulator specifications

Information


Unique identifier OMICS_06856
Name EvolSimulator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for EvolSimulator

EvolSimulator in publications

 (5)
PMCID: 4929450
PMID: 27363362
DOI: 10.1038/srep28970

[…] near future., for all programs mentioned below, default settings were used unless otherwise specified. we simulated sets of genomes using two different programs depending on their functionality: evolsimulator to simulate scenarios relevant to lateral genetic transfer (lgt), and alf to simulate genome rearrangement. evolsimulator allows the user to specify rates independently for speciation, […]

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

[…] and can be then visualized and analyzed using nettest ., under codon models, ω can change across codons., coding sequences are simulated by nucleotide substitution models, avoiding stop codons., evolsimulator simulates phylogenetic histories under the birth-death model of speciation and extinction ., under codon models, ω can change across codons and branches., amino acid models implemented […]

PMCID: 3224671
PMID: 21092133
DOI: 10.1186/1471-2148-10-360

[…] graph. following this, we formulate several candidate techniques for computing comparison genomes, several variants of which are based on lp. details of the parameter settings used for blast and evolsimulator can be found in the methods section., an intergenomic affinity graph g for a set of genomes c = {c1, c2, ..., cm} is defined as a set of vertices v = {v1, v2, ..., vm}, […]

PMCID: 2851118
PMID: 20808525
DOI: 10.2174/138920210790218007

[…] under more or less complex models of dna sequence evolution, for example dawg [] allows for the inclusion of indels the same as simgenome [], which also includes integrated parameter estimation. evolsimulator [] is also phylogenetic based model, which evolves prokaryote genomes allowing lateral gene transfer. the above methods are specially focused on the impact of the different mentioned […]

PMCID: 2760874
PMID: 18840304
DOI: 10.1186/gb-2008-9-10-r147

[…] [] and evolveagene []; of these, indel-seq-gen offers the most realism, with rate heterogeneity and a diverse set of mutations. simulators for genomic sequence (including conserved features) include evolsimulator [], which simulates gene family dynamics, and pspe [], which simulates turnover in promoter regions., many of these model-based simulation tools share a fundamental deficiency […]


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EvolSimulator institution(s)
Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada

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