backtrans_align.help

usage: seqmagick backtrans-align [-h] [-o destination_file]
                                 [-t {standard-ambiguous,vertebrate-mito,standard}]
                                 [-a {fail,warn,none}]
                                 protein_align nucl_align

Given a protein alignment and unaligned nucleotides, align the nucleotides
using the protein alignment. Protein and nucleotide sequence files must
contain the same number of sequences, in the same order, with the same IDs.

positional arguments:
  protein_align         Protein Alignment
  nucl_align            FASTA Alignment

optional arguments:
  -h, --help            show this help message and exit
  -o destination_file, --out-file destination_file
                        Output destination. Default: STDOUT
  -t {standard-ambiguous,vertebrate-mito,standard}, --translation-table {standard-ambiguous,vertebrate-mito,standard}
                        Translation table to use. [Default: standard-
                        ambiguous]
  -a {fail,warn,none}, --fail-action {fail,warn,none}
                        Action to take on an ambiguous codon [default: fail]