NAME¶

pxrevcomp - reverse complement sequences

SYNOPSIS¶

pxrevcomp [OPTIONS]... [FILE]...

DESCRIPTION¶

Reverse complement sequences. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN. Results are written in fasta format.

OPTIONS¶

-s, --seqf=FILE

input sequence file, STDIN otherwise

-i, --ids=IDS

a comma sep list of ids to flip (NO SPACES!)

-g, --guess

EXPERIMENTAL: guess whether there are seqs that need to be rev comp. uses edlib library on first seq

-p, --pguess

EXPERIMENTAL: progressively guess

-m, --sguess

EXPERIMENTAL: sampled guess

-o, --outf=FILE

output sequence file, STOUT otherwise

-h, --help

display this help and exit

-V, --version

display version and exit

-C, --citation

display phyx citation and exit

CITATION¶

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

AUTHOR¶

Written by Stephen A. Smith (blackrim)

REPORTING BUGS¶

Report bugs to: <https://github.com/FePhyFoFum/phyx/issues> phyx home page: <https://github.com/FePhyFoFum/phyx>

COPYRIGHT¶

Copyright © 2017-2021 FePhyFoFum License GPLv3