PhyloSort : Phylogenetic Tree Sorting

PhyloSort is a Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units (OTUs). In September 2012, PhyloSort migrated from Sourceforge to GitHub.

Features

• Searching for monophyletic relationship among groups of taxa.
• Filtering by bootstrap support values associated with the monophyletic clades.
• Filtering by tree complexity (number of taxa in a tree).
• Filtering by family complexity (number of genes per taxon in a tree).
• Clustering trees (genes) into tree clusters (gene families).
• Grouping OTUs using a taxonomy reference tree.
• Clean and reusable implementation of common tasks to manipulate a Newick phylogenetic tree data structure such as parsing, traversal and, rerooting.
• Visualizing tree topology using ATV, now Archaeopteryx.