.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH ALL_DISTS "1" "May 2016" "all_dists 1.4" "User Commands"
.SH NAME
all_dists \- Given a tree in Newick (*.nh) format, report distances
.SH DESCRIPTION
Given a tree in Newick (*.nh) format, report distances
between all pairs of leaves.
If multiple files are given,
then distances are computed by averaging across models,
and statistics describing the errors in the estimates
are reported (can be useful for bootstrapping; see
\&'phyloBoot \fB\-\-dump\-mods\fR').
.SH USAGE
all_dists <tree.nh> [<tree2.nh> <tree3.nh>...]
.SH OPTIONS
.HP
\fB\-\-mod\fR, \fB\-m\fR
.IP
Read from tree model (*.mod) file(s) instead of Newick file.
.HP
\fB\-\-tree\fR, \fB\-t\fR <file>|<string>
.TP
Use leaf names from given tree.
Useful when primary files
.IP
use numbers rather than names.
.HP
\fB\-\-help\fR, \fB\-h\fR
Print this help message.