pxclsq - clean positions or taxa with too much ambiguous data

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

       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 © 2015-2024 FePhyFoFum License GPLv3

pxclsq 1.3.1                                        June 2024                                          PXCLSQ(1)

       Clean  alignments  by removing positions/taxa with too much ambiguous data.  This will take fasta, fastq,
       phylip, and nexus formats from a file or STDIN.  Results are written in fasta format.

       pxclsq - clean positions or taxa with too much ambiguous data

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

       -p, --prop=DOUBLE
              proportion required to be present, default=0.5

       -e, --empty
              remove columns that are completely empty (- or ?)

       -m, --min=INT
              the minimum number of good characters required per site - a min of 1 is equivalent to -e above

       -t, --taxa
              consider missing data per taxon (default: per site)

       -c, --codon
              examine sequences by codon rather than site - requires all sequences be in frame  and  of  correct
              length

       -i, --info
              report counts of missing data and exit - combine with -t to get report by taxon (rather than site)
              - combine with -c to use codons as units

       -v, --verbose
              more verbose output (i.e. if entire seqs are removed)

       -o, --outf=FILE
              output fasta file, STOUT otherwise

       -h, --help
              display this help and exit

       -V, --version
              display version and exit

       -C, --citation
              display phyx citation and exit

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

pxclsq [OPTIONS]...