Man page - pxclsq(1)

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Manual

PXCLSQ

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
CITATION
AUTHOR
REPORTING BUGS
COPYRIGHT

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>