TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information. (January 2014)

• Record Type: Journal Article
• Authors: Struck, Torsten H.
• Is Part Of: Evolutionary bioinformatics online. Volume 10(2014)
• Publication Date: 2014-01
• Subjects: phylogenomics -- paralogy -- biases -- long-branch attraction -- conflict detection -- tree based; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.4137/EBO.S14239
• Languages: English
• ISSNs: 1176-9343

Abstract

Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available athttp://www.annelida.de/research/bioinformatics/software.html .