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)

last-dotplot 1542                                 February 2024                                  LAST-DOTPLOT(1)