title: YBYRÁ facilitates comparison of large phylogenetic trees.
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 .
authors.affiliation: Inter-institutional Grad Program on Bioinformatics, University of São Paulo, Rua do Matão, tv. 14, no. 101, sala 137, São Paulo, 05508-090, Brazil. machadodj@usp.br.
authors.forename: Denis Jacob
authors.initials: DJ
authors.lastname: Machado
mesh_terms: D005075:Biological Evolution; D003198:Computer Simulation; D006801:Humans; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software