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Setting up

• Installation and dependencies

CDSKIT commands

• accession2fasta: Retrieving fasta sequences from a list of GenBank accessions

• aggregate: Extracting the longest sequences combined with a sequence name regex

• backtrim: Back-translating a trimmed protein alignment

• gapjust: Adjusting consecutive Ns to the fixed length

• hammer: Removing less-occupied codon columns from a gappy alignment

• intersection: Dropping non-overlapping sequence labels between two sequences files or between a sequence file and a gff file

• label: Modifying sequence labels

• mask: Masking ambiguous and/or stop codons

• pad: Making nucleotide sequences in-frame by head and tail paddings

• parsegb: Converting the GenBank format

• printseq: Print a subset of sequences with a regex

• rmseq: Removing a subset of sequences by using a sequence name regex and by detecting problematic sequence characters

• split: Splitting 1st, 2nd, and 3rd codon positions

• stats: Printing sequence statistics