pxcat(1)

manual page for pxcat 1.3

Section 1 phyx bookworm source

Description

PXCAT

NAME

pxcat - manual page for pxcat 1.3

SYNOPSIS

pxcat [OPTIONS]... FILES

DESCRIPTION

Sequence file concatenation. Can use wildcards e.g.:

pxcat -s *.phy -o my_cat_file.fa

However, if the argument list is too long (shell limit), put filenames in afile:

for x in *.phy

do echo $x >> flist.txt

done

and call using the -f option:

pxcat -f flist.txt -o my_cat_file.fa

This will take fasta, fastq, phylip, and nexus sequence formats. Individual files may be of different formats.

OPTIONS

-s, --seqf=FILE

list of input sequence files (space delimited)

-f, --flistFILE

file listing input files (one per line)

-p, --partf=FILE

output partition file, none otherwise

-u, --uppercase

export characters in uppercase

-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 F. Walker, 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>