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Setting up

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