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