cdskit maxalign

cdskit maxalign removes sequences to maximize codon-based alignment area, inspired by MaxAlign (Gouveia-Oliveira et al. 2007).

CDSKIT computes alignment area in codon units (3 nt):

alignment area = (number of retained sequences) x (number of complete codon sites)

A complete codon site is a codon column where every retained sequence has no missing character in that codon.

Example

In this example, CDSKIT removes one gap-heavy sequence and keeps codon sites that are complete in the retained set.

Command

cdskit maxalign --seq_file input.fasta --out_file output.fasta --mode exact

input.fasta

>seq1
ATGAAACCCGGG
>seq2
ATGAAACCCGGG
>seq3
ATGAAACCCGGG
>seq4
---AAA---GGG

output.fasta

>seq1
ATGAAACCCGGG
>seq2
ATGAAACCCGGG
>seq3
ATGAAACCCGGG

Key options

• --mode auto|exact|greedy: Solver mode. auto uses exact search for small inputs and greedy search for larger inputs.
• --max_exact_sequences INT: Maximum number of sequences allowed in exact mode (default: 16).
• --missing_chars STR: Characters treated as missing within a codon (default: -?.).
• --keep_seq_name_regex REGEX [REGEX ...]: Never remove matching sequence IDs.
• --max_removed INT: Maximum number of sequences that may be removed.
• --report PATH: Optional JSON or TSV optimization report. Empty input writes an empty sequence output and a zero-count report.

TSV report format

TSV reports use schema version 2 and begin with schema_version and section. summary rows contain run-level metrics; step rows describe the initial state and each removal step. List-valued removed_ids cells are JSON arrays.

Notes

• Input sequences should already be aligned (equal sequence lengths).
• Input sequence lengths should be multiples of three.
• Output keeps only retained sequences and codon sites that are complete in the retained set.
• --mode auto switches to greedy when the number of input sequences exceeds --max_exact_sequences.

References

Cite the method or resource actually used and report the CDSKIT version and options.

• Gouveia-Oliveira R, Sackett PW, Pedersen AG (2007). MaxAlign: maximizing usable data in an alignment. BMC Bioinformatics 8:312. Paper — Original alignment-area objective; CDSKIT adapts the objective to codons and supplies its own solvers.