.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH LAST-DOTPLOT "1" "January 2019" "last-dotplot 963" "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\-v\fR, \fB\-\-verbose\fR
show progress messages & data about the plot
.TP
\fB\-x\fR INT, \fB\-\-width\fR=\fI\,INT\/\fR
maximum width in pixels (default: 1000)
.TP
\fB\-y\fR INT, \fB\-\-height\fR=\fI\,INT\/\fR
maximum height in pixels (default: 1000)
.TP
\fB\-m\fR M, \fB\-\-maxseqs\fR=\fI\,M\/\fR
maximum number of horizontal or vertical sequences
(default=100)
.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\-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)
.TP
\fB\-\-alignments\fR=\fI\,FILE\/\fR
secondary alignments
.TP
\fB\-\-sort1\fR=\fI\,N\/\fR
genome1 sequence order: 0=input order, 1=name order,
2=length order, 3=alignment order (default=1)
.TP
\fB\-\-sort2\fR=\fI\,N\/\fR
genome2 sequence order: 0=input order, 1=name order,
2=length order, 3=alignment order (default=1)
.TP
\fB\-\-strands1\fR=\fI\,N\/\fR
genome1 sequence orientation: 0=forward orientation,
1=alignment orientation (default=0)
.TP
\fB\-\-strands2\fR=\fI\,N\/\fR
genome2 sequence orientation: 0=forward orientation,
1=alignment orientation (default=0)
.TP
\fB\-\-max\-gap1\fR=\fI\,FRAC\/\fR
maximum unaligned (end,mid) gap in genome1: fraction
of aligned length (default=0.5,2)
.TP
\fB\-\-max\-gap2\fR=\fI\,FRAC\/\fR
maximum unaligned (end,mid) gap in genome2: fraction
of aligned length (default=0.5,2)
.TP
\fB\-\-pad\fR=\fI\,FRAC\/\fR
pad length when cutting unaligned gaps: fraction of
aligned length (default=0.04)
.TP
\fB\-\-border\-pixels\fR=\fI\,INT\/\fR
number of pixels between sequences (default=1)
.TP
\fB\-\-border\-color\fR=\fI\,COLOR\/\fR
color for pixels between sequences (default=black)
.TP
\fB\-\-margin\-color\fR=\fI\,COLOR\/\fR
margin color
.IP
Text options:
.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: 14)
.TP
\fB\-\-labels1\fR=\fI\,N\/\fR
genome1 labels: 0=name, 1=name:length,
2=name:start:length, 3=name:start\-end (default=0)
.TP
\fB\-\-labels2\fR=\fI\,N\/\fR
genome2 labels: 0=name, 1=name:length,
2=name:start:length, 3=name:start\-end (default=0)
.TP
\fB\-\-rot1\fR=\fI\,ROT\/\fR
text rotation for the 1st genome (default=h)
.TP
\fB\-\-rot2\fR=\fI\,ROT\/\fR
text rotation for the 2nd genome (default=v)
.IP
Annotation options:
.TP
\fB\-\-bed1\fR=\fI\,FILE\/\fR
read genome1 annotations from BED file
.TP
\fB\-\-bed2\fR=\fI\,FILE\/\fR
read genome2 annotations from BED file
.TP
\fB\-\-rmsk1\fR=\fI\,FILE\/\fR
read genome1 repeats from RepeatMasker .out or
rmsk.txt file
.TP
\fB\-\-rmsk2\fR=\fI\,FILE\/\fR
read genome2 repeats from RepeatMasker .out or
rmsk.txt file
.IP
Gene options:
.TP
\fB\-\-genePred1\fR=\fI\,FILE\/\fR
read genome1 genes from genePred file
.TP
\fB\-\-genePred2\fR=\fI\,FILE\/\fR
read genome2 genes from genePred file
.TP
\fB\-\-exon\-color\fR=\fI\,COLOR\/\fR
color for exons (default=PaleGreen)
.TP
\fB\-\-cds\-color\fR=\fI\,COLOR\/\fR
color for protein\-coding regions (default=LimeGreen)
.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: orange)