SIDIER: substitution and indel distances to infer evolutionary relationships

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Authors Antonio JesusMunoz-Pajares
Journal/Conference Name Methods in Ecology and Evolution
Paper Category
Paper Abstract Summary 1. The amount of evolutionary information in phylogeogr aphic studies is usually limited due to the low diver-gence between closely related organisms. Consequently, obtaining the maximum evolutionary information con-tainedinsequencealignmentswouldbeofgreatimportancetoinferphylogeographicrelationships.2. SIDIER is asoftware package that allows inferring evolutionary relationships from gapped alignments usinginformationcontainedinbothsubstitutionsandinsertions/deletions(indels).3. SIDIER estimates the number of indel events that occurred during sequence evolution to obtain a distancematrix. This indel distance matrix may be combined with the substitution distance matrix calculated separatelyfromthesamedataset.4. Usingthissoftware,theinferredevolutionaryeventscanberepresentedbymeans ofpercolationnetworks.5. SIDIER is written in the open source R language and is freely available through the Comprehensive RArchiveNetwork(http://cran.r-project.org/web/packages/sidier/index.html). Key-words: evolutionarybiology,molecularevolution,phylogenetics,phylogeographyIntroduction
Date of publication 2013
Code Programming Language R
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