tcsBU: a tool to extend TCS network layout and visualization

António Múrias dos Santos; Maria Pilar Cabezas; Ana Isabel Tavares; Raquel Xavier; Madalena Branco

doi:10.1093/bioinformatics/btv636

tcsBU: a tool to extend TCS network layout and visualization

Bioinformatics. 2016 Feb 15;32(4):627-8. doi: 10.1093/bioinformatics/btv636. Epub 2015 Oct 29.

Authors

António Múrias dos Santos¹, Maria Pilar Cabezas², Ana Isabel Tavares¹, Raquel Xavier³, Madalena Branco²

Affiliations

¹ Faculdade de Ciências da Universidade do Porto, 4169-007 Porto, Portugal CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal and.
² CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal and.
³ CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal and School of Biological Sciences, Cardiff University, Cardiff, CF10 3AX, UK.

PMID: 26515821
DOI: 10.1093/bioinformatics/btv636

Abstract

Motivation: TCS is a widely used haplotype network reconstruction software, but lacks the capability of overlapping genetic with geographic structure, which is often a first step in phylogeographic analysis.

Results: tcsBU is a web-based program that extends the capabilities of TCS, by implementing haplotype classification into an arbitrary user-defined scheme, which is displayed as pie-chart like graphs embedded into the network. Taking advantage of modern graphic libraries, tcsBU also improves the speed at which the final network layout is reached. Networks can be saved as a Scalable Vector Graphics format.

Availability and implementation: tcsBU is available on-line at http://cibio.up.pt/software/tcsBU/. The source code is freely available from https://github.com/sairum/tcsbu/ under a standard MIT license.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Graphics
Haplotypes*
Software*