pxlssq - print sequence file summary

Author

       Written by Joseph F. Walker, Joseph W. Brown

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 © 2016-2024 FePhyFoFum License GPLv3

pxlssq 1.3.1                                        June 2024                                          PXLSSQ(1)

Description

       Print  sequence  file summary.  By default returns all properties. Alternatively choose 1 property.  This
       will take fasta, phylip, and nexus formats from a file or STDIN.

Name

       pxlssq - print sequence file summary

Options

-s, --seqf=FILE
              input seq file, STDIN otherwise

       -i, --indiv
              output stats for individual sequences

       -n, --nseq
              return the number of sequences

       -c, --nchar
              return the number of characters (only if aligned) - for unaligned seqs, use with -i flag

       -l, --labels
              return all taxon labels (one per line)

       -p, --prot
              force interpret as protein (if inference fails)

       -a, --aligned
              return whether sequences are aligned (same length)

       -f, --freqs
              return character state frequencies

       -m, --missing
              return the proportion of missing (-,?) characters

       -o, --outf=FILE
              output stats 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>