NAME

       pxclsq - clean positions or taxa with too much ambiguous data

SYNOPSIS

       pxclsq [OPTIONS]...

DESCRIPTION

       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.

OPTIONS

       -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

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.

AUTHOR

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

REPORTING BUGS

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

COPYRIGHT

       Copyright © 2015-2024 FePhyFoFum License GPLv3

pxclsq 1.3.1                                        June 2024                                          PXCLSQ(1)