CLEARCUT(1)

💖 CLEARCUT(1) — the manual, but make it make sense 💖

okay bestie, sit down, hydrate, because we're about to talk about Clearcut — that's the clearcut command from the User Commands section of your manual, and it does Relaxed Neighbor Joining. no cap. she's a phylogenetics girlie and she EATS. 🌳✨

🦋 SYNOPSIS 🦋

clearcut --in=<infilename> --out=<outfilename> [options]...

that's it. that's the whole vibe check. you give her an in file, you give her an out file, you sprinkle options on top like glitter. 💅

🌸 DESCRIPTION 🌸

so basically Clearcut takes your data (a distance matrix OR an alignment, we'll get there) and builds you a tree. relaxed neighbor joining style. she's flexible, she's fast, she's iconic. let's break down every single knob and dial, because I refuse to let you run her on defaults and then cry to me about it. 🫶

✨ GENERAL OPTIONS ✨

• -h, --help — displays this information. the "help me I'm lost" button. use it. love it.
• -V, --version — prints the version of this program. so you know exactly which queen you're talking to.
• -v, --verbose — more output. (Default: OFF) — she's quiet by nature, this makes her yap.
• -q, --quiet — silent operation. (Default: ON) — the default. she's not doing small talk unless asked.
• -s, --seed=<seed> — explicitly set the PRNG seed to a specific value. you want reproducible randomness? set the seed, bestie, and she'll do the exact same thing every time.
• -r, --norandom — attempt joins deterministically. (Default: OFF) — no dice rolls, just vibes and rules.
• -S, --shuffle — randomly shuffle the distance matrix. (Default: OFF) — she shuffles the matrix like a playlist. chaos, but organized chaos.
• -N, --neighbor — use the traditional Neighbor-Joining algorithm. (Default: OFF) — the classic recipe instead of the relaxed one.

💜 INPUT OPTIONS 💜

• -I, --stdin — read input from STDIN. pipe it in, queen.
• -d, --distance — input file is a distance matrix. (Default: ON) — this is the default, so if you say nothing, this is what she assumes.
• -a, --alignment — input file is a set of aligned sequences. (Default: OFF)
• -D, --DNA — input alignment are DNA sequences.
• -P, --protein — input alignment are protein sequences.

🧚 CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction) 🧚

okay so listen. by default she applies NO correction. zero. none. if you want her to correct the distance matrix on the way in, you gotta pick a model yourself. 👑

• -j, --jukes — use Jukes-Cantor correction for computing the distance matrix.
• -k, --kimura — use Kimura correction for the distance matrix.

🔥 OUTPUT OPTIONS 🔥

• -O, --stdout — output tree to STDOUT. tree goes straight to your terminal, no file needed.
• -m, --matrixout=<file> — output distance matrix to specified file. so you can see the matrix she built.
• -n, --ntrees=<n> — output n trees. (Default: 1) — she'll hand you more than one tree if you ask nicely.
• -e, --expblen — exponential notation for branch lengths. (Default: OFF)
• -E, --expdist — exponential notation in distance output. (Default: OFF)

🌈 EXAMPLES 🌈

compute tree by supplying a distance matrix via stdin:

clearcut --distance < distances.txt > treefile.tre

compute tree by supplying an alignment of DNA sequences from a file:

clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre

like, that second one? that's the whole workflow. alignment in, tree out, main character energy. 😭💖

heads up bestie: --distance is the default input mode and --quiet is the default output mode, so you're not being weird for leaning on defaults — you're just being efficient. ✨

and that's the page!! Clearcut Version: 1.0.9, dated February 2014, from the CLEARCUT(1) manual itself. she's been serving trees since 2014 and she has not missed once. go build something gorgeous. 🌳💅🎀