cdskit hammer

cdskit hammer removes sparsely occupied codon columns from an aligned CDS. With an integer --nail N, a codon column is retained when at least N sequences translate to a non-missing amino acid there. Translated -, ?, X, and * do not count as occupied. Use --nail all to require occupancy in every sequence. This translation-based rule differs from the strict ACGT-only clean-codon rule used by trimcodon.

Example

Command

cdskit hammer --seq_file input.fasta --out_file output.fasta --nail 4

input.fasta

>seq1
---ATGTAAATTATGTTGAAG---TGATGA---------
>seq2
---ATGTNAATTATGTTGAAG---TATTGA---------
>seq3
---ATGTGAATTATGTTGAAG---TATTGA---------
>seq4
---ATGTAAATT---TTGANG---TATTGATTTTCATCA
>seq5
---ATGTAAATTATGTTGANG---TATTGATTTTCATCA
>seq6
---ATGTAAATT---TTGANG---TATTGATTTTCATCA

output.fasta

>seq1
ATGATTATGTTGTGA
>seq2
ATGATTATGTTGTAT
>seq3
ATGATTATGTTGTAT
>seq4
ATGATT---TTGTAT
>seq5
ATGATTATGTTGTAT
>seq6
ATGATT---TTGTAT

Key options

• --nail INT/all controls the occupancy threshold (4 by default).
• --prevent_gap_only yes may lower the threshold when the requested value would leave a sequence containing gaps only. Set it to no for strict threshold application.
• --codon_table INT selects the genetic code used by codon-aware checks.

Input must be an aligned nucleotide sequence set whose lengths are multiples of three.

References

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

• Fukushima K, Pollock DD (2023). Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence. Nature Ecology & Evolution 7:155–170. Paper — Published CDSKIT workflow context; describes pad, mask, backtrim and hammer, not all later options.