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Compute Multiple Sequence Alignments for Orthogroups

orthogroupMSA.Rd

Aligns orthologous gene sequences across species using an external alignment tool (MAFFT or Kalign). Alignments are computed for each orthogroup and saved as FASTA files.

Usage

orthogroupMSA(data, method = "mafft", nbThreads = 1, nbThreadsByOrthogroup = 1)

Arguments

data

List. Experiment object from newExperiment containing:

orthogroups

GRanges with orthogroupID metadata.

dirs$dna

Directory containing input FASTA files from orthogroupDNA.

dirs$msa

Output directory for alignment files.

method

Character. Alignment tool to use:

  • "mafft" (default): MAFFT with automatic algorithm selection.

  • "kalign": Kalign3 (faster, less accurate for divergent sequences).

nbThreads

Integer. Total number of threads available. Multiple orthogroups are aligned in parallel using nbThreads / nbThreadsByOrthogroup workers. Default: 1.

nbThreadsByOrthogroup

Integer. Threads allocated to each alignment job. Default: 1.

Value

Invisibly returns a character vector of paths to the generated MSA files.

Details

The function implements a two-level parallelization strategy:

  • Outer level: Multiple orthogroups are processed in parallel.

  • Inner level: Each alignment tool uses multiple threads.

The number of parallel orthogroup jobs is floor(nbThreads / nbThreadsByOrthogroup).

For example, with nbThreads = 8 and nbThreadsByOrthogroup = 2, 4 orthogroups are aligned simultaneously, each using 2 threads.

Output Files

Alignments are written to data$dirs$msa as:

  • <orthogroupID>_msa.fa: FASTA format, one file per orthogroup.

System Requirements

The selected alignment tool must be installed and available in PATH:

See also

orthogroupDNA to extract sequences (previous step), loadMSA to load alignments.

Examples

if (FALSE) { # \dontrun{
data <- newExperiment(sampleInfo, speciesInfo, orthogroups,
                      dnaDir, msaDir, speciesTree)
orthogroupDNA(data, nbThreads = 4)

# Align with MAFFT (8 threads total, 2 per alignment = 4 parallel jobs)
orthogroupMSA(data, method = "mafft", nbThreads = 8, nbThreadsByOrthogroup = 2)

# Check output
list.files(data$dirs$msa, pattern = "_msa.fa$")
} # }