SoRT2

SoRT2 computes genome rearrangement distances and infers phylogenetic trees from linear or circular multi-chromosomal gene orders to analyze structural variations such as reversals, generalized transpositions, and translocations (fusions and fissions) and their impact on evolutionary relationships.

Key Features:

• Input format: Accepts two or more linear or circular multi-chromosomal gene orders in a FASTA-like format.
• Supported rearrangements: Handles reversals, generalized transpositions, and translocations (including fusions and fissions).
• Pairwise rearrangement distance: Computes rearrangement distance for two genomes and provides an optimal scenario highlighting the specific genes involved in each rearrangement operation.
• Phylogenetic tree construction: Builds phylogenetic trees from a matrix of pairwise genome rearrangement distances using Neighbor-Joining (NJ), UPGMA, and Fitch-Margoliash (FM) methods.
• Statistical support: Computes jackknife support values for NJ, UPGMA, and FM trees.

Scientific Applications:

• Genome evolution analysis: Investigating mechanisms of genome evolution by analyzing structural rearrangements.
• Phylogenetic inference: Inferring phylogenetic relationships among species or strains based on genome rearrangement distances.
• Comparative genomics: Identifying conserved genomic regions and recurrent rearrangement patterns across organisms.

Methodology:

Pairwise distances are calculated from structural rearrangements (reversals, generalized transpositions, translocations including fusions and fissions), with an optimal scenario reported for two-genome comparisons specifying genes involved in each operation; a matrix of pairwise distances is used to infer trees via Neighbor-Joining, UPGMA, and Fitch-Margoliash, and jackknife resampling is applied to compute support values.