cdskit mask

cdskit mask replaces ambiguous codons, stop codons, and partial-gap codons with a repeated mask character while preserving the reading frame. Complete gap codons (---) remain gaps.

Example

Command

cdskit mask --seq_file input.fasta --out_file output.fasta

input.fasta

>stop
---ATGTAAATTATGTTGAAG---
>ambiguous1
---ATGTNAATTATGTTGAAG---
>ambiguous2
---ATGT-AATTATGTTGAAG---
>all
---ATGTAAATT--GTTGANG---

output.fasta

>stop
---ATGNNNATTATGTTGAAG---
>ambiguous1
---ATGNNNATTATGTTGAAG---
>ambiguous2
---ATGNNNATTATGTTGAAG---
>all
---ATGNNNATTNNNTTGNNN---

Key options

• --mask_char CHAR sets the replacement character (N by default); it is repeated three times for each masked codon.
• --ambiguous_codon yes|no controls masking of codons that cannot be resolved under the selected genetic code (yes by default).
• --stop_codon yes|no controls stop-codon masking (yes by default).
• --codon_table INT selects the genetic code.

Input must be nucleotide data with every sequence length divisible by three. Partial-gap codons such as AT- are masked even when both optional masking switches are set to no.

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.