last-dotplot1

Usage

Overview

Draw a dotplot of pair-wise sequence alignments.

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

--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=1,4)

--max-gap2=FRAC

maximum unaligned (end,mid) gap in genome2: fraction of aligned length (default=1,4)

--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)

-a FILE, --bed1=FILE, --rmsk1=FILE, --genePred1=FILE, --gap1=FILE

read genome1 annotations

-b FILE, --bed2=FILE, --rmsk2=FILE, --genePred2=FILE, --gap2=FILE

read genome2 annotations

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)

Color options:

-c COLOR, --forwardcolor=COLOR

color for forward alignments (default: red)

-r COLOR, --reversecolor=COLOR

color for reverse alignments (default: blue)

--border-color=COLOR

color for pixels between sequences (default=black)

--margin-color=COLOR

margin color

--exon-color=COLOR

color for exons (default=PaleGreen)

--cds-color=COLOR

color for protein-coding regions (default=LimeGreen)

--bridged-color=COLOR

color for bridged gaps (default: yellow)

--unbridged-color=COLOR

color for unbridged gaps (default: orange)