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Keywords:

  • evolutionary biology;
  • molecular evolution;
  • phylogenetics;
  • phylogeography

Summary

  1. 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.
  2. SIDIER is a software package that allows inferring evolutionary relationships from gapped alignments using information contained in both substitutions and insertions/deletions (indels).
  3. 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.
  4. Using this software, the inferred evolutionary events can be represented by means of percolation networks.
  5. 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).