phyloSkeleton

phyloSkeleton automates selection, retrieval, annotation, marker identification, and preparation of genome sequences to support phylogenomic tree inference and comparative evolutionary analyses.

Key Features:

• Taxon Selection: Uses taxonomy and assembly quality rules to select representative genomes that provide appropriate taxon density across phylogenomic trees.
• Data Retrieval: Integrates with public genomic databases NCBI and JGI to retrieve genome sequences directly.
• Marker Identification: Identifies genetic markers within retrieved genomes to generate datasets for multiple sequence alignment.
• Annotation and File Preparation: Performs genome annotation as needed and prepares files formatted for multiple sequence alignment.

Scientific Applications:

• Evolutionary Biology and Genomics: Facilitates construction of phylogenetic trees to infer species relationships and evolutionary histories by automating preparatory steps such as taxon selection, genome retrieval, marker identification, and alignment file preparation.

Methodology:

Implemented as a Perl module, it applies predefined criteria based on taxonomy and assembly quality for genome selection, integrates with NCBI and JGI for sequence retrieval, performs genome annotation and marker identification, and prepares files for multiple sequence alignment.