Palestra: YBYRÁ facilitates comparison of large phylogenetic trees

[Denis Jacob Machado]

Boa tarde, gente!

Algumas pessoas me pediram para dar uma palestra sobre o YBYRÁ e como utilizá-lo para analisar resulstados de análises filogenéticas. Teremos então uma palestra hoje sobre isso, às 17h00, na sala 158 da Zoologia. Vocês estão todos convidados mas, como está bem em cima da hora, não exitem em apenas dar um pulo na minha mesa caso queiram usar o programa alguma hora e tenham dificuldades.

Abraços, Denis

Artigo disponível em: www.biomedcentral.com/1471-2105/16/204

Programas disponíveis em: http://www.ib.usp.br/grant/anfibios/researchSoftware.html

Manual: https://gitlab.com/MachadoDJ/ybyra/wikis/home

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.

Denis Jacob Machado

about.me/machadodj
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Laboratório de Anfíbios