PHLAWD

PHLAWD constructs large phylogenetic datasets from NCBI's GenBank using a megaphylogeny approach to enable analysis of diversification patterns across broad taxonomic groups.

Key Features:

• Implementation: Implemented in C++ for scalable phylogenetic dataset assembly.
• Data Integration: Integrates sequence data and taxon records from NCBI's GenBank to build input datasets for phylogenetic inference.
• Megaphylogeny methodology: Leverages a megaphylogeny approach to assemble comprehensive trees encompassing thousands of species and assumes GenBank representation is proportional to biodiversity within major clades.
• Scalability: Supports construction of ultra-large phylogenies and can be applied to smaller backbone trees for comparative analyses.

Scientific Applications:

• Diversification rate analysis: Comparing small backbone trees with mega-phylogenies to detect shifts in diversification rates and their associations with taxonomic groups.
• Angiosperm clade studies: Generation of large phylogenies for clades such as Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae for macroevolutionary analyses.

Methodology:

PHLAWD constructs phylogenetic datasets from NCBI's GenBank and contrasts two approaches: Small backbone trees with a limited number of extant species per terminal clade, and a mega-phylogeny approach exemplified by a constructed tree of 55,473 seed plant species derived from GenBank.