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)