trees-consensus(1)

💖 trees-consensus — the manual, but make it cute 💖

okay bestie, welcome to trees-consensus(1) — yes the whole manual page, and yes i'm about to make consensus trees sound like the most iconic thing you've ever met. because honestly? they kinda are. 🦋

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✨ NAME ✨

trees-consensus — find consensus trees and supported splits. that's it. that's the whole job. and she eats every time. 💅

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🌸 SYNOPSIS 🌸

trees-consensus [OPTIONS] sampled-trees [sampled-trees ...
sampled-trees]

so you hand her some sampled trees (one or more files, she's greedy like that) and optionally some OPTIONS, and she does her little magic. no cap.

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🎀 DESCRIPTION 🎀

Find consensus trees and supported splits.

fr fr, that's the whole vibe. she reads in your sampled trees, and she gives you back consensus trees and the splits that are actually supported. main character energy only. 👑

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🫶 INPUT OPTIONS: 🫶

these are the "what do i feed her" options. she's not picky but she does have boundaries.

• -h, --help — produce help message. she'll tell you what's up. 🥺
• -V, --verbose — output more log messages on stderr. she gets chatty. she's just excited to be here.
• -s arg (=10%), --skip arg (=10%) — number of trees to skip. default is 10% so she doesn't get bored of the beginning. 🙈
• -u arg, --until arg — read until this number of trees. she stops when she's had enough.
• -m arg, --max arg — thin tree samples down to this number of trees. slimming down, but make it phylogenetics.
• -x arg (=1), --subsample arg (=1) — factor by which to subsample. default 1, aka no skipping, she's taking everything in.
• -i arg, --ignore arg — comma-separated list of taxa to ignore. not them. not today. 💀

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🌈 REPORTING OPTIONS: 🌈

what she tells you when she's done, and where she puts it.

• --map-trees arg (=1) — only report the top arg trees per file. default is 1, so she's being selective, as she should.
• --min-support arg (=0.25) — minimum threshold PP for splits. default 0.25. lowkey a low bar, but that's her business.
• --report arg — write supported partitions to file arg.
• --map-tree arg — write out the map tree to file arg.
• --consensus arg — write out consensus trees.
• --greedy-consensus arg — write out greedy consensus trees. she's not like other girls, she's greedy.
• --extended-consensus-L arg — write out extended consensus trees + lengths.
• --extended-consensus arg — write out extended consensus trees.
• --support-levels arg — write #branches versus LOD to file arg.
• --extended-support-levels arg — write #sub-branches versus LOD to file arg.

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🔥 SEARCH OPTIONS: 🔥

the detective era. 🔍

• --sub-partitions — search for partial splits.
• --depth arg (=1) — depth at which to look for partial splits. default 1.
• --rooting arg (=0.9) — threshold in search for partial splits. default 0.9.
• --odds-ratio arg (=1.5) — report partial-splits only if removing taxa improves the odds by at least this ratio. default 1.5. she's got standards.

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💜 EXAMPLES: 💜

this is the part where she shows off. watch and learn, bestie.

Compute the majority consensus tree, skipping the first 10% of trees:

% trees-consensus newick.trees > c50.tree
% trees-consensus newick.trees --skip=10% > c50.tree

Skip the first 100 trees:

% trees-consensus newick.trees --skip=100 > c50.tree

Skip the first 20% of trees and take every 10th tree thereafter:

% trees-consensus newick.trees --skip=20% -x10 > c50.tree

Compute the 50% (majority) and 80% consensus trees:

% trees-consensus newick.trees --consensus=0.5:c50.tree,0.8:c80.tree
% trees-consensus newick.trees --consensus=0.5,0.8:c80.tree > c50.tree

Compute the MAP tree and write a summary of supported partitions:

% trees-consensus --map-tree=MAP.tree --report=partitions.txt

Compute the MAP tree and write it to the standard output:

% trees-consensus --map-tree=- --report=partitions.txt

okay but notice how --map-tree=- sends it to standard output. the dash is the moment. ⭐

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😭 REPORTING BUGS: 😭

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.

(if something's broken, tell them, don't just suffer in silence, i'm begging 🥺)

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👑 AUTHORS 👑

Benjamin Redelings. that's the icon. that's the legend. thank you for your service. 🫡

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and that's the whole page, bestie — trees-consensus(1), from Feb 2018, part of the BAli-Phy family, delivered with love and zero skipped details. periodt. 💖✨