.\" DO MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH PARSINSERT "1" "February 2014" "parsinsert 1.04" "User Commands"
.SH NAME
ParsInsert \- Parsimonious Insertion of unclassified sequences into phylogenetic tree
.SH DESCRIPTION
.PP
\fBparsinsert [options]  <insert_sequences>\fR
.PP
Perform Insertion of Sequences into Given Tree
.HP
\fB\-m\fR <mask file>           \- read mask from this file
.TP
\fB\-s\fR <tree sequences>      \- read core tree sequences from this file
(default: PI_Tree.fasta)
.TP
\fB\-t\fR <tree file>           \- read core tree from this file
(default: PI_Tree.tree)
.HP
\fB\-x\fR <tree taxonomy>       \- read core tree taxomony from this file
.TP
\fB\-o\fR <output file>         \- output taxonomy for each insert sequence to this file
(default: PI_Results.log)
.HP
\fB\-l\fR [\-|<log file>]         \- create log file (default is ParsInsert.log)
.HP
\fB\-n\fR#                      \- number of best matches to display
.HP
\fB\-c\fR#                      \- percent threshold cutoff
.HP
\fB\-p\fR                       \- print node comments in newick file
.HP
\fB\-D\fR#                      \- print branch lengths using # decimal places
tree sequence file: PI_Tree.fasta
.SH LICENSE
Copyright (C) 2007\-2011 David Knox

This program comes with ABSOLUTELY NO WARRANTY

This is free software, and you are welcome to redistribute under certain 
conditions \- see /usr/share/common-licenses/GPL-3.