EvolveAGene protocols

View EvolveAGene computational protocol

EvolveAGene statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Coalescent simulation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

EvolveAGene specifications

Information


Unique identifier OMICS_15341
Name EvolveAGene
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes

Versioning


Add your version

Publication for EvolveAGene

EvolveAGene in pipeline

2016
PMCID: 4864206
PMID: 27167125
DOI: 10.1371/journal.pntd.0004712

[…] [] by uploading the genbank-formatted files for each genome. we considered genes from all regions designated as “intact”, “incomplete” or “questionable” by phast as prophage genes in our analysis., evolveagene 3 [] was used for gene-by-gene simulation of mutations under neutrality. ten rounds of simulation were performed per gene. in each round, a random tree topology (with every branch […]


To access a full list of citations, you will need to upgrade to our premium service.

EvolveAGene in publications

 (4)
PMCID: 4864206
PMID: 27167125
DOI: 10.1371/journal.pntd.0004712

[…] [] by uploading the genbank-formatted files for each genome. we considered genes from all regions designated as “intact”, “incomplete” or “questionable” by phast as prophage genes in our analysis., evolveagene 3 [] was used for gene-by-gene simulation of mutations under neutrality. ten rounds of simulation were performed per gene. in each round, a random tree topology (with every branch […]

PMCID: 3901687
PMID: 24475074
DOI: 10.1371/journal.pone.0086088

[…] were co-stained with anti-cd4 and l-pha-fitc to detect the mgat5 gene product . staining profiles showed a near normal distribution for all species., to explore the potential in near-nxs/t sites, the evolveagene 3.05 algorithm was used to generate sequence diversity by mutagenesis and random selection of specific sequences . the following settings were used: topology = symmetric; number of taxa =  […]

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

[…] example, which generates data of a given dinucleotide content (with a somewhat constrained choice of substitution model), is sissiz []. protein simulators include simprot [], indel-seq-gen [] 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 […]

PMCID: 1828704
PMID: 17367204
DOI: 10.1371/journal.pcbi.0030051

[…] aligned []. the failure to include indels in the simulation process therefore reduces considerably the confidence we can place in applying conclusions drawn from those simulations to real data., the evolveagene simulation program [,] was designed to mimic the evolution of sequences in a more biologically realistic fashion. a real sequence is used for the root node of the tree, and a strictly […]


To access a full list of publications, you will need to upgrade to our premium service.

EvolveAGene institution(s)
Bellingham Research Institute, Bellingham, WA, USA

EvolveAGene reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review EvolveAGene