| Full text | |
| Author(s): |
Machado, Denis Jacob
[1]
Total Authors: 1
|
| Affiliation: | [1] Univ Sao Paulo, Inter Inst Grad Program Bioinformat, BR-05508090 Sao Paulo - Brazil
Total Affiliations: 1
|
| Document type: | Journal article |
| Source: | BMC Bioinformatics; v. 16, JUL 1 2015. |
| Web of Science Citations: | 7 |
| 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 ``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) | |
| FAPESP's process: | 12/10000-5 - A multi-disciplinary approach to the study of amphibian diversification |
| Grantee: | Taran Grant |
| Support Opportunities: | Research Grants - Young Investigators Grants |
| FAPESP's process: | 13/05958-8 - Comparative Genomics and the Evolution of Amphibian Chemical Defense |
| Grantee: | Denis Jacob Machado |
| Support Opportunities: | Scholarships in Brazil - Doctorate |
| FAPESP's process: | 09/13561-5 - Phylogenetic diversity the lineages of Acanthobothrium van Beneden, 1850 (Eucestoda: Tetraphyllidea: Onchobothriidae) parasites of Potamotrygonidae (Chondrichthyes: Myliobatoidei) |
| Grantee: | Denis Jacob Machado |
| Support Opportunities: | Scholarships in Brazil - Master |