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Number of citations per year for the bioinformatics software tool iGTP
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Protocols

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 citations

 (5)
library_books

Reconstructing evolutionary trees in parallel for massive sequences

2017
BMC Syst Biol
PMCID: 5751538
PMID: 29297337
DOI: 10.1186/s12918-017-0476-3

[…] andled, 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 of mul […]

library_books

Multilocus inference of species trees and DNA barcoding

2016
PMCID: 4971187
PMID: 27481787
DOI: 10.1098/rstb.2015.0335

[…] on 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 usin […]

library_books

A Bayesian Supertree Model for Genome Wide Species Tree Reconstruction

2014
Syst Biol
PMCID: 4851173
PMID: 25281847
DOI: 10.1093/sysbio/syu082

[…] sensus 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 for each g […]

library_books

Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next Gen Data

2013
Genome Biol Evol
PMCID: 3845638
PMID: 24148944
DOI: 10.1093/gbe/evt157

[…] methods, but this taxon was placed confidently (100% bootstrap) within the Saturniidae in every analysis, corroborating previous morphological and molecular hypotheses (e.g., , ; , ). Fig. 3.—The MDC iGTP analysis that minimizes deep coalescence placed B. mori as sister to Plodia interpunctella, which appears misplaced, as these taxa belong in different superfamilies and no previous phylogenetic a […]

library_books

Fast and accurate methods for phylogenomic analyses

2011
BMC Bioinformatics
PMCID: 3283310
PMID: 22152123
DOI: 10.1186/1471-2105-12-S9-S4

[…] stimating species trees from estimated gene trees or gene tree distributions. Four of these are based upon ILS, and include Glass (from Phylonet v. 2.3), Phylonet-MDC v. 2.3 (here called “Phylonet”), iGTP-MDC v. 1.1, and BUCKy v. 1.4.0. The other three methods are Greedy, iGTP-Dup v. 1.1 and iGTP-Duploss v. 1.1. All of these methods, except BUCKy, take as input a single tree for each gene. In cont […]


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

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