SIDIER: substitution and indel distances to infer evolutionary relationships
Article first published online: 18 NOV 2013
© 2013 The Author. Methods in Ecology and Evolution © 2013 British Ecological Society
Methods in Ecology and Evolution
Volume 4, Issue 12, pages 1195–1200, December 2013
How to Cite
Muñoz-Pajares, A. J. (2013), SIDIER: substitution and indel distances to infer evolutionary relationships. Methods in Ecology and Evolution, 4: 1195–1200. doi: 10.1111/2041-210X.12118
- Issue published online: 9 DEC 2013
- Article first published online: 18 NOV 2013
- Accepted manuscript online: 24 SEP 2013 10:46AM EST
- Manuscript Accepted: 11 SEP 2013
- Manuscript Received: 1 JUL 2013
- Spanish Ministry of Education and Science. Grant Number: FPU:AP2006-00685
- evolutionary biology;
- molecular evolution;
- The amount of evolutionary information in phylogeographic studies is usually limited due to the low divergence between closely related organisms. Consequently, obtaining the maximum evolutionary information contained in sequence alignments would be of great importance to infer phylogeographic relationships.
- SIDIER is a software package that allows inferring evolutionary relationships from gapped alignments using information contained in both substitutions and insertions/deletions (indels).
- SIDIER estimates the number of indel events that occurred during sequence evolution to obtain a distance matrix. This indel distance matrix may be combined with the substitution distance matrix calculated separately from the same data set.
- Using this software, the inferred evolutionary events can be represented by means of percolation networks.
- SIDIER is written in the open source R language and is freely available through the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/sidier/index.html).