NAME¶

pxrms - remove sequences by label

SYNOPSIS¶

pxrms [OPTIONS]...

DESCRIPTION¶

Remove sequences by label. 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 nucleotide sequence file, STDIN otherwise

-n, --names=CSL

names sep by commas (NO SPACES!)

-f, --namesf=FILE

names in a file (each on a line)

-r, --regex=STRING

match tip labels by a regular expression

-c, --comp

take the complement (i.e. remove any taxa not in list)

-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 Joseph W. Brown, Joseph F. Walker, 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 © 2015-2021 FePhyFoFum License GPLv3