positional arguments:¶

help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align

help

Detailed help for actions using help <action>

convert

Convert between sequence formats

info

Info action

mogrify

Modify sequence file(s) in place.

primer-trim

Find a primer sequence in a gapped alignment, trim to amplicon

quality-filter

Filter reads based on quality scores

extract-ids

Extract the sequence IDs from a file

backtrans-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.

optional arguments:¶

-h, --help

show this help message and exit

-V, --version

Print the version number and exit

-v, --verbose

Be more verbose. Specify -vv or -vvv for even more

-q, --quiet

Suppress output