LAST-DOTPLOT(1)

💖 last-dotplot — the manual page, but make it cute 💖

okay bestie, so last-dotplot lives in section 1 of the manual (User Commands, yk the classics) and honestly? she's iconic. she makes dotplots. that's the whole vibe. let's get into it 🫶

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✨ NAME ✨

last-dotplot — make a dotplot (a.k.a. Oxford Grid 🌈 no, literally, that's what it's called) of alignments in LAST tabular format. slay.

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🎀 SYNOPSIS 🎀

the way she's called, fr fr:

last-dotplot --help
last-dotplot [options] maf-or-psl-or-tab-alignments
last-dotplot [options] maf-or-psl-or-tab-alignments dotplot.png|gif|...

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🦋 DESCRIPTION 🦋

bestie. she draws a dotplot of pair-wise sequence alignments. that's it. that's the whole job. and she EATS every single time 💅

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👑 OPTIONS 👑

okay this is the long part, grab a snack 🍓 every single flag is here, no skips, no cap.

• -h, --help — shows this help message, then dips. exits, basically. courtesy of argparse, we stan
• -v, --verbose — she gets chatty: shows progress messages and data about the plot. main character commentary ✨
• -x INT, --width=INT — maximum width in pixels (default: 1000). she's not getting wider than this, periodt.
• -y INT, --height=INT — maximum height in pixels (default: 1000). same energy, vertical edition.
• -m M, --maxseqs=M — maximum number of horizontal or vertical sequences (default=100). more than that and it's giving chaos 😭
• -1 PATTERN, --seq1=PATTERN — which sequences to show from the 1st genome. you pick, she respects it 🫶
• -2 PATTERN, --seq2=PATTERN — which sequences to show from the 2nd genome. twin flags, twin energy.
• --alignments=FILE — secondary alignments. extra alignments, extra drama.
• --sort1=N — genome1 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1). lowkey name order is the moment.
• --sort2=N — genome2 sequence order: 0=input order, 1=name order, 2=length order, 3=alignment order (default=1). yes bestie, same menu, second genome.
• --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). note the comma, bestie — it's 1,4, not a typo 🫶
• --max-gap2=FRAC — maximum unaligned (end,mid) gap in genome2: fraction of aligned length (default=1,4). again with the comma. iconic.
• --pad=FRAC — pad length when cutting unaligned gaps: fraction of aligned length (default=0.04). a lil cushion 🌸
• -j N, --join=N — join: 0=nothing, 1=alignments adjacent in genome1, 2=alignments adjacent in genome2 (default=0). she can bridge the girls together if u want 💅
• --border-pixels=INT — number of pixels between sequences (default=1).
• -a FILE, --bed1=FILE, --rmsk1=FILE, --genePred1=FILE, --gap1=FILE — read genome1 annotations. five names, one job. she contains multitudes.
• -b FILE, --bed2=FILE, --rmsk2=FILE, --genePred2=FILE, --gap2=FILE — read genome2 annotations. the genome2 twin, obviously.

✨ Text options ✨

text is a whole personality, ok?

• -f FILE, --fontfile=FILE — TrueType or OpenType font file. pick ur font, serve looks 🎀
• -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). horizontal, as she should.
• --rot2=ROT — text rotation for the 2nd genome (default=v). vertical, for the aesthetic 💫

🌈 Color options 🌈

the part we've all been waiting for. the glam team.

• -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. (no default listed, so she leaves it up to u, bestie)
• --exon-color=COLOR — color for exons (default=PaleGreen). 🍵
• --cds-color=COLOR — color for protein-coding regions (default=LimeGreen). the coding girls get their own shade, deserved.
• --bridged-color=COLOR — color for bridged gaps (default: yellow). 💛
• --unbridged-color=COLOR — color for unbridged gaps (default: orange). 🧡

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and that's the whole page, bestie. every flag, every default, every comma, we did not skip a single one, no cap 💜

this lil legend is last-dotplot version 1654, dated August 2026 — so yeah, she's fresh, she's current, she's serving. ttys, and go make a dotplot 💅✨🦋