Artículos de revistas
YBYRÁ facilitates comparison of large phylogenetic trees
Fecha
2015Registro en:
BMC Bioinformatics. 2015 Jul 01;16(1):204
10.1186/s12859-015-0642-9
Autor
Machado, Denis Jacob
Institución
Resumen
Abstract
Background
The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals.
Results
The “YBYRÁ” project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist).
Conclusions
YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at
http://www.ib.usp.br/grant/anfibios/researchSoftware.html
.