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LAST-DOTPLOT(1) User Commands LAST-DOTPLOT(1)

NAME

last-dotplot - make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format

SYNOPSIS

last-dotplot --help
last-dotplot [options] maf-or-tab-alignments dotplot.png
last-dotplot [options] maf-or-tab-alignments dotplot.gif
...

DESCRIPTION

Draw a dotplot of pair-wise sequence alignments in MAF or tabular format.

OPTIONS

-h, --help
show this help message and exit
-v, --verbose
show progress messages & data about the plot
-x INT, --width=INT
maximum width in pixels (default: 1000)
-y INT, --height=INT
maximum height in pixels (default: 1000)
-m M, --maxseqs=M
maximum number of horizontal or vertical sequences (default=100)
-1 PATTERN, --seq1=PATTERN
which sequences to show from the 1st genome
-2 PATTERN, --seq2=PATTERN
which sequences to show from the 2nd genome
-c COLOR, --forwardcolor=COLOR
color for forward alignments (default: red)
-r COLOR, --reversecolor=COLOR
color for reverse alignments (default: blue)
--alignments=FILE
secondary alignments
--sort1=N
genome1 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
--sort2=N
genome2 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1)
--strands1=N
genome1 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
--strands2=N
genome2 sequence orientation: 0=forward orientation, 1=alignment orientation (default=0)
--max-gap1=FRAC
maximum unaligned (end,mid) gap in genome1: fraction of aligned length (default=0.5,2)
--max-gap2=FRAC
maximum unaligned (end,mid) gap in genome2: fraction of aligned length (default=0.5,2)
--pad=FRAC
pad length when cutting unaligned gaps: fraction of aligned length (default=0.04)
-j N, --join=N
join: 0=nothing, 1=alignments adjacent in genome1, 2=alignments adjacent in genome2 (default=0)
--border-pixels=INT
number of pixels between sequences (default=1)
--border-color=COLOR
color for pixels between sequences (default=black)
--margin-color=COLOR
margin color
Text options:
-f FILE, --fontfile=FILE
TrueType or OpenType font file
-s SIZE, --fontsize=SIZE
TrueType or OpenType font size (default: 14)
--labels1=N
genome1 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
--labels2=N
genome2 labels: 0=name, 1=name:length, 2=name:start:length, 3=name:start-end (default=0)
--rot1=ROT
text rotation for the 1st genome (default=h)
--rot2=ROT
text rotation for the 2nd genome (default=v)
Annotation options:
--bed1=FILE
read genome1 annotations from BED file
--bed2=FILE
read genome2 annotations from BED file
--rmsk1=FILE
read genome1 repeats from RepeatMasker .out or rmsk.txt file
--rmsk2=FILE
read genome2 repeats from RepeatMasker .out or rmsk.txt file
Gene options:
--genePred1=FILE
read genome1 genes from genePred file
--genePred2=FILE
read genome2 genes from genePred file
--exon-color=COLOR
color for exons (default=PaleGreen)
--cds-color=COLOR
color for protein-coding regions (default=LimeGreen)
Unsequenced gap options:
--gap1=FILE
read genome1 unsequenced gaps from agp or gap file
--gap2=FILE
read genome2 unsequenced gaps from agp or gap file
--bridged-color=COLOR
color for bridged gaps (default: yellow)
--unbridged-color=COLOR
color for unbridged gaps (default: orange)
December 2020 last-dotplot 1169