.TH FATHOM "1" "October 2013" "fathom 2010-07-28" "User Commands"
.SH NAME
fathom \- sequence and annotation tool
.SH SYNOPSIS
.B fathom
<\fBann\fR> <\fBdna\fR> <\fBcommands\fR>
.SH OPTIONS
.TP
\fB\-help\fR
report useful information
.HP
\fB\-validate\fR [\-quiet]
.HP
\fB\-gene\-stats\fR [\-errors\-ok \fB\-nucleotide\fR \fB\-dinucleotide]\fR
.HP
\fB\-categorize\fR <int>
.HP
\fB\-export\fR <int> [\-plus \fB\-errors\-ok]\fR
.HP
\fB\-extract\fR <feature> \fB\-length\fR <int> \fB\-offset\fR <int>
.HP
\fB\-exon\-intron\fR
.HP
\fB\-split\fR <\-number <int> | \fB\-training\fR <float> | \fB\-GC\fR <float> | \fB\-repeat\fR <float>>
.HP
\fB\-ace\-format\fR <\-gene\-method <string> [\-dna \fB\-extra\fR <string>]>
.HP
\fB\-compare\-genes\fR <predictions> [\-details]
.HP
\fB\-score\-genes\fR <hmm> [\-errors\-ok]
.HP
\fB\-filter\-genes\fR <hmm> \fB\-min\-score\fR <float> \fB\-min\-length\fR <int>