.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH LAST-DOTPLOT "1" "January 2017" "last-dotplot 830" "User Commands"
.SH NAME
last-dotplot \- make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format
.SH SYNOPSIS
.B last-dotplot
\fI\,--help\/\fR
.br
.B last-dotplot
[\fI\,options\/\fR] \fI\,maf-or-tab-alignments dotplot.png\/\fR
.br
.B last-dotplot
[\fI\,options\/\fR] \fI\,maf-or-tab-alignments dotplot.gif\/\fR
.br
.B ...

.SH DESCRIPTION
Draw a dotplot of pair\-wise sequence alignments in MAF or tabular format.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-1\fR PATTERN, \fB\-\-seq1\fR=\fI\,PATTERN\/\fR
which sequences to show from the 1st genome
.TP
\fB\-2\fR PATTERN, \fB\-\-seq2\fR=\fI\,PATTERN\/\fR
which sequences to show from the 2nd genome
.TP
\fB\-x\fR WIDTH, \fB\-\-width\fR=\fI\,WIDTH\/\fR
maximum width in pixels (default: 1000)
.TP
\fB\-y\fR HEIGHT, \fB\-\-height\fR=\fI\,HEIGHT\/\fR
maximum height in pixels (default: 1000)
.TP
\fB\-f\fR FILE, \fB\-\-fontfile\fR=\fI\,FILE\/\fR
TrueType or OpenType font file
.TP
\fB\-s\fR SIZE, \fB\-\-fontsize\fR=\fI\,SIZE\/\fR
TrueType or OpenType font size (default: 11)
.TP
\fB\-c\fR COLOR, \fB\-\-forwardcolor\fR=\fI\,COLOR\/\fR
color for forward alignments (default: red)
.TP
\fB\-r\fR COLOR, \fB\-\-reversecolor\fR=\fI\,COLOR\/\fR
color for reverse alignments (default: blue)
.IP
Unsequenced gap options:
.TP
\fB\-\-gap1\fR=\fI\,FILE\/\fR
read genome1 unsequenced gaps from agp or gap file
.TP
\fB\-\-gap2\fR=\fI\,FILE\/\fR
read genome2 unsequenced gaps from agp or gap file
.TP
\fB\-\-bridged\-color\fR=\fI\,COLOR\/\fR
color for bridged gaps (default: yellow)
.TP
\fB\-\-unbridged\-color\fR=\fI\,COLOR\/\fR
color for unbridged gaps (default: pink)