BaCoCa

BaCoCa identifies compositional and codon-frequency biases in aligned sequence data to inform and improve phylogenomic analyses.

Key Features:

• Bias detection: Detects compositional biases and codon-frequency variation in aligned sequence data.
• Statistical approaches: Implements Relative Codon Frequency Variation (RCFV) and C value calculations to assess sequence biases.
• Input file support: Accepts widely used input formats including FASTA and relaxed PHYLIP.
• Partition and subset analysis: Processes hundreds of predefined gene partitions and taxon subsets within a single run.
• Output compatibility: Produces tab-delimited summary output files for downstream analysis in programs such as R and Excel.
• Visualization: Generates heat maps with hierarchical clustering using R.

Scientific Applications:

• Phylogenomic bias identification: Identifies sequence-compositional and codon-frequency biases that can mislead phylogenetic reconstructions.
• Multilocus dataset assessment: Evaluates bias across large multilocus datasets, gene partitions, and taxon subsets to support dataset curation and interpretation.

Methodology:

Computes Relative Codon Frequency Variation (RCFV) and C value calculations on aligned FASTA or relaxed PHYLIP inputs, produces tab-delimited summary outputs, and can generate heat maps with hierarchical clustering using R while processing predefined gene partitions and taxon subsets.