PhyloSort 1.3

PhyloSort by Ahmed Moustafa is a specialized tool for rapidly screening and organizing large collections of phylogenetic trees based on user-defined taxonomic patterns and branch-support criteria. Designed for genome-scale studies, it helps researchers pinpoint trees that contain target clades (for example, monophyletic groups), exclude unwanted taxa, and meet minimum support thresholds—accelerating tasks like hypothesis testing, ortholog curation, and discovery of horizontal or endosymbiotic gene transfer signals.

Key capabilities:

• Batch filtering of thousands of trees using flexible rules (e.g., “group A is monophyletic and exclusive,” “includes at least one taxon from group B,” “excludes any from group C”).
• Support-aware queries, allowing minimum bootstrap or other support cutoffs for clades of interest.
• Compatibility with standard phylogenetic tree formats such as Newick.
• Clear outputs, including the subset of matching trees and summary reports that document which criteria were satisfied.
• Easy integration into phylogenomics pipelines for reproducible, large-scale analysis.

Typical use cases:

• Rapidly identifying trees consistent with a specified evolutionary hypothesis.
• Detecting candidate horizontal or endosymbiotic gene transfers by enforcing presence/absence patterns across taxa.
• Quality control and triage of gene families prior to detailed manual curation.

PhyloSort streamlines the otherwise time-consuming process of manually inspecting trees, enabling efficient, criteria-driven selection that scales to modern phylogenomic datasets.

PhyloSort is developed by Ahmed Moustafa. The most popular version of this product among our users is 1.3. The name of the program executable file is phylosort.exe.