Man page - last-dotplot(1)

Packages contains this manual

Package:  last-align
apt-get install last-align

Manuals in package:
• maf-cut(1)
• lastdb(1)
• last-train(1)
• last-pair-probs(1)
• last-merge-batches(1)
• maf-join(1)
• lastal(1)
• fasta-nr(1)
• maf-swap(1)
• last-map-probs(1)
• maf-convert(1)
• last-postmask(1)
• fastq-interleave(1)
• maf-sort(1)
• last-split(1)
• last-dotplot(1)
Documentations in package:
• last-align

Manual

LAST-DOTPLOT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

---

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)

---