YBYRA facilitates comparison of large phylogenetic trees

Autor(es)

Machado, Denis Jacob ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inter Inst Grad Program Bioinformat, BR-05508090 Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: BMC Bioinformatics; v. 16, JUL 1 2015.
• Citações Web of Science: 7

Resumo

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 ``YBYRA{''} 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. YBYRA 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: YBYRA 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. (AU)

• Processo FAPESP: 12/10000-5 - Uma abordagem multidisciplinar para o estudo da diversificação de anfíbios
• Beneficiário: Taran Grant
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 13/05958-8 - Genômica Comparada e a Evolução da Defesa Química em Anfíbios
• Beneficiário: Denis Jacob Machado
• Modalidade de apoio: Bolsas no Brasil - Doutorado
• Processo FAPESP: 09/13561-5 - Diversidade filogenética das linhagens de Acanthobothrium van Beneden, 1850 (Eucestoda: Tetraphyllidea: Onchobothriidae) parasitas de Potamotrygonidae (Chondrichthyes: Myliobatoidei)
• Beneficiário: Denis Jacob Machado
• Modalidade de apoio: Bolsas no Brasil - Mestrado