EasyCGTree

EasyCGTree reconstructs genome-scale maximum-likelihood phylogenies from prokaryotic core gene sets to infer evolutionary relationships.

Key Features:

• Implementation: Implemented in Perl and distributed with precompiled standalone executables of external programs.
• Profile HMM-based homolog search: Constructs a profile HMM database (PHD) and uses profile HMMs for homolog identification.
• Custom gene sets: Supports user-supplied gene sets and integration of user-built profiles into the PHD.
• Phylogenetic reconstruction approaches: Generates maximum-likelihood trees using both supermatrix (SM) and supertree (ST) approaches and provides a consensus-tree option as a variant of SM.
• Validation and benchmarking: Validated on 43 Paracoccus genomes with cophenetic correlation coefficients (CCC) > 0.99 and shown to produce nearly identical topology to UBCG and bcgTree (distance < 0.1).

Scientific Applications:

• Prokaryotic phylogeny reconstruction: Inferring evolutionary relationships among prokaryotic genomes using core-gene phylogenies.
• Comparative microbial genomics: Performing genome-scale phylogenomic analyses to compare microbial genomes.
• Pipeline benchmarking and topology comparison: Comparing tree topologies and benchmarking against pipelines such as UBCG and bcgTree.

Methodology:

Profile HMM-based homolog searching against a profile HMM database (PHD), construction of supermatrix and supertree maximum-likelihood phylogenies, and optional consensus-tree generation; implemented in Perl.