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.
Highlights
The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis
While previous work suggests that Gene tree parsimony (GTP) can produce accurate species trees [8,12,13,14,15,16,17,18], currently available software is either too slow to handle large data sets or lacks the flexibility to handle the wide range of evolutionary processes that affect gene tree topologies
We introduce iGTP, a stand-alone software application with an easy-to-use graphical user interface (Figure 1) that makes it possible to conduct large-scale gene tree parsimony analyses on hundreds of taxa and thousands of gene phylogenies for three of the most important variants of the GTP problem: (i) the duplication problem [7,25,26,27,28,29,30,31,32], which minimizes the number of gene duplications, (ii) the duplication-loss problem [7,25,26,27,28,29,30,31,32,33,34], which minimizes the number of gene duplications and losses, and (iii) the deep-coalescence problem [17,35,36], which minimizes the number of deep coalescences
Summary
We 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. We 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. IGTP provides a user-friendly graphical interface with integrated tree visualization software to facilitate analysis of the results. Conclusions: iGTP 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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