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PXCAT(1)

User Commands

PXCAT(1)

NAME¶

pxcat - sequence file concatenation

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 a file:¶

: 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, --flist=FILE: 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>

COPYRIGHT¶

Copyright © 2015-2021 FePhyFoFum License GPLv3

July 2023

pxcat 1.3