SeqFIRE

SeqFIRE extracts sequence features and indel regions from multiple protein sequence alignments to identify conserved blocks, indels (insertions and deletions), and fast-evolving sites for phylogenomic analyses.

Key Features:

• Automated Indel Extraction: Identifies and extracts indels (insertions and deletions) from protein sequence alignments as phylogenetic markers.
• Conserved Block Identification: Extracts blocks of conserved alignment columns to delineate stable regions across sequences.
• Fast-Evolving Site Detection: Detects fast-evolving sites using a combination of conservation metrics and entropy calculations.
• Parameter Customization: Allows adjustment of major variables for indel detection, conserved block extraction, and site-rate identification.
• Comprehensive Output Options: Produces numbered indel lists, alignments in NEXUS format with options for annotated or removed indels, and matrices containing only indel information.

Scientific Applications:

• Phylogenomics: Enables analysis of large multigene datasets to incorporate indel and conserved-block information into phylogenetic inference.
• Phylogenetic Marker Discovery and Molecular Evolution: Facilitates identification of novel phylogenetic markers and assessment of molecular evolutionary patterns using indels and fast-evolving sites.

Methodology:

Analyzes multiple sequence alignments to extract conserved and variable regions and uses algorithms that combine conservation metrics and entropy calculations to identify indels and fast-evolving sites; outputs include numbered indel lists, NEXUS-formatted alignments with annotated or removed indels, and indel-only matrices.