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 inputs. Individual files can be of different formats.

-s, --seqf=FILE

list of input sequence files (space delimited)

-f, --flistFILE

file listing input files (one per line)

-o, --outf=FILE

output sequence file, stout otherwise

-p, --partf=FILE

output partition file, none otherwise

-h, --help

display this help and exit

-V, --version

display version and exit