cognac

cognac aligns and concatenates shared genes from input genomes to produce concatenated gene alignments for phylogenetic analysis of large genomic datasets.

Key Features:

• Concatenated Gene Alignments: Identifies shared genes across input genomes, aligns each marker gene with MAFFT, and concatenates individual alignments into a single core-gene alignment.
• Multi-threading and Algorithmic Optimizations: Employs multi-threading and algorithmic optimizations to scale to thousands of genomes and reduce runtime.
• Scalability Demonstration: Has produced core-gene alignments for over 11,000 Escherichia genomes comprising 1,353 genes in under 17 hours.
• R Package Implementation: Provided as an R package implementation for integration into R-based analysis workflows.
• Customizable Parameters: Exposes configurable parameters to adapt marker selection and alignment behavior for different datasets.

Scientific Applications:

• Microbial Phylogenomics: Supports large-scale phylogenetic analyses in microbial genomics by generating concatenated alignments from many genomes.
• Phylogenetic Inference: Produces inputs suitable for robust phylogenetic tree reconstruction from core-gene datasets.
• Evolutionary and Genomic Studies: Enables investigation of species evolution, genetic diversity, and signals of horizontal gene transfer from concatenated gene alignments.

Methodology:

Identifies shared genes across input genomes, aligns each marker gene individually using MAFFT, concatenates the individual alignments into a single alignment, and leverages multi-threading and algorithmic optimizations; implemented as an R package.