EXTRACTBCITREES(1)

✨ extractBCITrees ✨

okay bestie, gather round, because this one is literally from the mauveAligner package and it's about to read every tree and its posterior out of a whole pile of MrBayes .trprobs files 🎀 no cap, that's the whole job description.

🌸 NAME 🌸

extractBCITrees — part of the mauveAligner package, and it reads all the trees and their posterior from a set of MrBayes .trprobs files 🦋

💅 SYNOPSIS 💅

extractBCITrees <random seed> <BCI threshold> <max output trees>
<MrBayes .trprobs input file 1 .. N> <nexus output file>

like… it wants a lot of args, but we move 💖

👑 DESCRIPTION 👑

okay so here's the tea, and it's genuinely good tea 🍓:

This program reads all the trees and their posterior from a set of MrBayes .trprobs files, and then it sums and normalizes the posteriors for each topology. Iconic behaviour, honestly.

Then, all the trees that meet a Bayes Credible Interval threshold get saved — up to some maximum number of trees, because we do have limits 🫶

Here's the deets on the args, bestie:

• <BCI Threshold> — a number between 0 and 1 giving the BCI threshold. 0.9 is a good choice ✨ (fr fr, it's a vibe)
• <max output trees> — limit the output to this many trees. Keep it cute, keep it bounded 💅

⚠️ big important one, don't skip this: all trees in the input file must have the same number of taxa and the same taxon labels 😭 if they don't match up, that's not gonna slay, that's gonna be a whole mess.

🦋 that's it, that's the page 🦋

and now for the cute sign-off: this is version extractBCITrees 1.2.0+4713, dated April 2015 🌈 which means it's been serving these trees for literal years and it's still that girl 💜 periodt.