.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PXCLSQ "1" "May 2018" "pxclsq 0.99+ds" "User Commands"
.SH NAME
pxclsq \- Cleans alignments by removing positions with too much ambiguous data.
.SH SYNOPSIS
.B pxclsq
[\fI\,OPTION\/\fR]...
.SH DESCRIPTION
Cleans alignments by removing positions with too much ambiguous data.
This will take fasta, fastq, phylip, and nexus inputs.
Results are written in fasta format.
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input sequence file, stdin otherwise
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output fasta file, stout otherwise
.TP
\fB\-p\fR, \fB\-\-prop\fR=\fI\,DOUBLE\/\fR
proportion required to be present, default=0.5
.TP
\fB\-a\fR, \fB\-\-aminoacid\fR
force interpret as protein (if inference fails)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
more verbose output (i.e. if entire seqs are removed)
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
display version and exit
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.