ALiBaSeq

ALiBaSeq extracts homologous sequences from FASTA contigs and SAM/BAM alignments using similarity search outputs (BLAST, HMMER, LASTZ) for targeted retrieval in phylogenetic and comparative genomic analyses.

Key Features:

• Flexible input compatibility: Accepts tab-delimited outputs from BLAST, HMMER, and LASTZ as well as alignment files in SAM/BAM format.
• Comprehensive homolog retrieval: Extracts orthologous sequences from annotated and unannotated genomic assemblies derived from low- or high-depth shotgun sequencing and target capture datasets.
• Parameter customization: Provides user-modifiable search and extraction parameters to adjust sensitivity and specificity.
• Performance evaluation: Evaluated on datasets including divergent insect species with well-curated genomes and loci ranging from highly conserved to variable, showing high gene recovery with maximal coverage and low false positive rates.

Scientific Applications:

• Phylogenomics: Retrieval of orthologous loci from whole-genome sequencing (WGS) data for species tree inference and comparative analyses.
• Deep-level phylogenetics: Targeted sequence retrieval at deep phylogenetic depths while mitigating false positives associated with amino-acid space searches.
• Cross-taxon comparative genomics: Extraction of homologs from both well-curated and unannotated assemblies across diverse taxa and evolutionary scales.

Methodology:

Parses similarity search outputs (BLAST, HMMER, LASTZ) or alignment files (SAM/BAM) to identify and extract homologous regions from genomic assemblies.