pxcat - sequence file concatenation

Author

       Written by Joseph F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)

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.

Copyright

       Copyright © 2015-2024 FePhyFoFum License GPLv3

pxcat 1.3.1                                         June 2024                                           PXCAT(1)

Description

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

              pxcat -s *.phy -o my_cat_file.fa

   However,iftheargumentlististoolong(shelllimit),putfilenamesinafile:
              for x in *.phy

              do echo $x >> flist.txt

              done

   andcallusingthe-foption:
              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.

Name

       pxcat - sequence file concatenation

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

Reporting Bugs

       Report      bugs      to:      <https://github.com/FePhyFoFum/phyx/issues>      phyx      home      page:
       <https://github.com/FePhyFoFum/phyx>