pxrls1

Usage

Overview

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.