AB12PHYLO

AB12PHYLO performs Maximum Likelihood phylogenetic inference from ABI trace (Sanger) sequencing data for multi-gene phylogeny-based species identification and genetic diversity analysis.

Key Features:

• End-to-End Workflow: Covers processing from raw ABI trace Sanger reads to phylogenetic tree generation and export.
• Quality Control and Trimming: Performs quality control and trimming of Sanger ABI trace data to retain high-quality sequences for analysis.
• Multiple Sequence Alignment (MSA): Generates multiple sequence alignments to align sequences prior to phylogenetic inference.
• Informative Site Extraction: Extracts informative sites from alignments for use in phylogenetic reconstruction.
• Phylogenetic Tree Construction: Constructs phylogenetic trees using Maximum Likelihood methods.
• BLAST Search Integration: Performs BLAST searches against reference databases, including type specimens, for sequence identification within the phylogeny.
• Summary Statistics Calculation: Calculates basic summary statistics for each gene included in the phylogenetic analysis.

Scientific Applications:

• Mycology and related disciplines: Construction of multi-gene phylogenies for species identification, taxonomic placement, and genetic diversity studies.

Methodology:

Implements a wrapper that integrates open-access tools and performs quality control and trimming of ABI Sanger traces; generates multiple sequence alignments; extracts informative sites; conducts Maximum Likelihood phylogenetic inference; executes BLAST searches against reference databases including type specimens; and computes basic per-gene summary statistics.