1 research outputs found
SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an
easy-to-use, high- throughput tool to describe the nearest neighbors to a node
of interest in a phylogenetic tree as well as the support value for the
relationship. The application is a command line utility that can be embedded
into a phylogenetic analysis pipeline or can be used as a subroutine within
another C++ program. As a test case, we applied this new tool to the published
phylome of Salinibacter ruber, a species of halophilic Bacteriodetes,
identifying 13 unique sister relationships to S. ruber across the 4589 gene
phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in
the majority of phylogenies, but 91 phylogenies showed a branch-supported
sister association between S. ruber and Archaea, an evolutionarily intriguing
relationship indicative of horizontal gene transfer. This test case
demonstrates how SICLE makes it possible to summarize the phylogenetic
information produced by automated phylogenetic pipelines to rapidly identify
and quantify the possible evolutionary relationships that merit further
investigation. SICLE is available for free for noncommercial use at
http://eebweb.arizona.edu/sicle/.Comment: 8 pages, 4 figures in journal submission forma