PHYLUCE

PHYLUCE processes targeted-enrichment sequence data to assemble contigs, identify conserved and ultraconserved genomic loci, and prepare alignments for phylogenomic inference across evolutionary timescales ranging from <5 Ma to >300 Ma.

Key Features:

• Data preprocessing: Assembles contigs from targeted-enrichment sequence data and identifies targeted loci amid off-target background sequences.
• Alignment preparation: Aligns enriched contigs representing conserved and ultraconserved genomic elements and prepares and manipulates alignments for downstream phylogenomic analysis.
• Taxonomic and temporal scale: Processes data across hundreds of species and across evolutionary timescales from <5 Ma to >300 Ma.
• Large-scale dataset processing: Handles large phylogenomic datasets efficiently for broad comparative analyses.

Scientific Applications:

• Phylogenomics: Collection and analysis of conserved genomic elements for inferring phylogenetic relationships.
• Evolutionary biology: Investigation of evolutionary patterns across shallow and deep timescales.
• Systematics: Resolution of systematic relationships among species using conserved loci.
• Comparative genomics: Comparative analyses of conserved and ultraconserved elements across diverse taxa.

Methodology:

Assembles contigs from sequence data, identifies targeted loci amid off-target background sequences, aligns enriched contigs representing conserved and ultraconserved elements, and prepares and manipulates alignments for downstream phylogenomic inference.