ArticleBMC bioinformatics2010
iGTP: a software package for large-scale gene tree parsimony analysis.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- Exact median-tree inference for unrooted reconciliation costs.BMC evolutionary biology · 2020Article
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.BMC evolutionary biology · 2019Article
- PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.Molecular biology and evolution · 2019Article
- Gene tree parsimony for incomplete gene trees: addressing true biological loss.Algorithms for molecular biology : AMB · 2018Article
- Reconstructing evolutionary trees in parallel for massive sequences.BMC systems biology · 2017Article
- IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count.Journal of molecular evolution · 2017Article
- Multilocus inference of species trees and DNA barcoding.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.Systematic biology · 2016Article
- SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.Systematic biology · 2016Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Supertrees Based on the Subtree Prune-and-Regraft Distance.Systematic biology · 2014Article
- Large-scale multiple sequence alignment and tree estimation using SATé.Methods in molecular biology (Clifton, N.J.) · 2014Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.
resultsWe introduce iGTP, a platform-independent software program that implements state-of-the-art algorithms that greatly speed up species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves the functionality and performance of existing gene tree parsimony software and offers advanced features such as building effective initial trees using stepwise leaf addition and the ability to have unrooted gene trees in the input. Moreover, iGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results.
conclusionsiGTP enables, for the first time, gene tree parsimony analyses of thousands of genes from hundreds of taxa using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient graphical user interface.
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