---
name: "last-dotplot"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/last-dotplot"
---

# last-dotplot(1)

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

## 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-psl-or-tab-alignments*\
 **last-dotplot** \[*options*\] *maf-or-psl-or-tab-alignments dotplot.png\|gif\|*...

## DESCRIPTION

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)