NAME

pxrls - taxon relabelling from alignments

SYNOPSIS

pxrls [OPTIONS]... FILES

DESCRIPTION

Taxon relabelling for alignments. This will take fasta, phylip, and nexus formats from a file or STDIN. Two ordered lists of taxa, -c (current) and -n (new) must be provided. Alternatively, a regex pattern (-p) and replacement (-r) text can be provided. Results are written in fasta format.

OPTIONS

-s, --seqf=FILE: input seq file, STDIN otherwise
-c, --cnames=FILE: file containing current taxon labels (one per line)
-n, --nnames=FILE: file containing new taxon labels (one per line)

-p, --pattern=STRING regex pattern to replace

-r, --replace=STRING replacement pattern

-v, --verbose: make the output more verbose
-o, --outf=FILE: output 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, Stephen A. Smith (blackrim)

REPORTING BUGS

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