iGTP specifications

Information


Unique identifier OMICS_06051
Name iGTP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for iGTP

iGTP in publications

 (4)
PMCID: 5751538
PMID: 29297337
DOI: 10.1186/s12918-017-0476-3

[…] and computer memory limitation often becomes the bottleneck., multiple sequence alignment is necessary for evolutionary tree software tools, including mega [], mafft [], sate-ii [], iq-tree [], igtp [], fasttree [], and phangorn []. most multiple sequence alignment tools cannot deal with massive sequences (eg. >10,000 sequences). therefore, evolutionary tree reconstruction independent […]

PMCID: 4971187
PMID: 27481787
DOI: 10.1098/rstb.2015.0335

[…] cost (gtp; []). these methods compute the number of deep coalescences, gdls or hgts necessary to explain the gene tree–species tree discordance, returning the species tree that minimizes them. the igtp program [] implements the reconciliation models for either ils or gdl, whereas sprsupertrees [] does the same for hgt. other types of methods that are focused on ils calculate distance trees […]

PMCID: 4851173
PMID: 25281847
DOI: 10.1093/sysbio/syu082

[…] methods like those implemented in bucky ()., gtp aims to find species tree that minimizes its total reconciliation cost with a given collection of gene tree topologies. here we used the software igtp (), which assumes that the disagreement between gene trees and the species tree is either due to dl, or to ils. an independent analysis was conducted under each assumption. igtp allows […]

PMCID: 3283310
PMID: 22152123
DOI: 10.1186/1471-2105-12-S9-S4

[…] sets [], but of unknown computational complexity when the gene trees are constrained to be on the same taxon set. heuristics for mdc have been implemented in various packages, including phylonet [], igtp [], and mesquite []. optimal solutions to mdc are not guaranteed to be statistically consistent, meaning that even with true trees for an unboundedly large number of genes, the species tree […]


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iGTP institution(s)
Department of Computer Science, Iowa State University, Ames, IA, USA

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