CAM

CAM generates alignment-free phylogenetic reconstructions by comparing codon aversion motifs—the sets of unused synonymous codons within genes—across species to infer evolutionary relationships.

Key Features:

• Alignment-Free Approach: Uses an alignment-free strategy that does not require sequence alignments or ortholog annotations.
• Codon Aversion Motifs: Constructs and compares sets of unused synonymous codons per gene to capture codon usage patterns across species.
• Phylogenetic Distance Calculation: Computes pairwise distances as one minus the ratio of shared motifs to the total number of motifs in the species with fewer motifs.
• Scalability and Efficiency: Validated on 229,742,339 genes from 23,428 species and exhibits greater computational efficiency than maximum likelihood methods while maintaining accuracy comparable to other alignment-free approaches.
• Phylogenetic Reconstruction: Produces trees using the neighbor-joining algorithm with topologies congruent with the Open Tree of Life and the NCBI Taxonomy Database.

Scientific Applications:

• Alignment-free phylogeny generation: Rapidly generate phylogenetic trees without sequence alignment.
• Large-scale comparative genomics: Analyze genomic datasets spanning thousands of species for broad evolutionary inference.
• Codon usage conservation analysis: Investigate codon usage patterns as conserved characters in phylogenomic studies.

Methodology:

Per species, CAM constructs codon aversion motif sets from all genes; it calculates pairwise distances using one minus the ratio of shared motifs to the total motifs in the species with fewer motifs; phylogenies are inferred using the neighbor-joining algorithm.