pxcat(1) · carta

Usage

pxcat [OPTIONS] ... FILES

Overview

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.

Releases

3 releases since Debian 10 (Buster); the text changed 2 times.

10
12
13

--citation since Debian 12 (Bookworm); --flist since Debian 13 (Trixie); --uppercase since Debian 12 (Bookworm); -C since Debian 12 (Bookworm); -u since Debian 12 (Bookworm).

--flistFILE until Debian 12 (Bookworm).