PPLACER(1)

💖 PPLACER(1) 💖

okay bestie, gather round, because today we're talking about pplacer — a User Commands classic, and honestly? she's iconic. 🦋

✨ NAME ✨

pplacer — place reads on a phylogenetic tree 🌳

like, you've got reads. you've got a tree. pplacer is gonna introduce them. matchmaking but make it phylogenetics. 💅

🌸 SYNOPSIS 🌸

pplacer [options] [alignment]

👑 OPTIONS 👑

no cap, there are a LOT of these. but every single one is here, so don't come for me. let's go, in order, no skips: ⭐

• -c — drop the path to your reference package right here. 📦
• -t — the reference tree filename goes here. 🌳
• -r — and this one's for the reference alignment filename. 🧬
• -s — hand her a phyml stats.txt or a RAxML info file and she'll take the model parameters from it. 📄
• -d — point at the directory that holds all your reference info. 📁
• -p — calculate posterior probabilities. yes ma'am. 🎲
• -m — the substitution model, bestie. Protein options: LG, WAG, or JTT. Nucleotides: GTR. 🧪
• --model-freqs — use the model's frequencies instead of the reference alignment's frequencies. 🔄
• --gamma-cats — how many categories for the discrete gamma model. 🔢
• --gamma-alpha — set the shape parameter for a discrete gamma model. 📐
• --ml-tolerance — 1st stage branch len optimization tolerance (2nd stage is 1e-5). Default: 0.01. 🎯
• --pp-rel-err — relative error for the posterior probability calculation. Default is 0.01. 📏
• --unif-prior — use a uniform prior instead of exponential. flat is a vibe. ➖
• --inform-prior — use an informative exponential prior based on rooted distance to leaves. 🍃
• --prior-lower — lower bound for the informative prior mean. Default is 0. ⬇️
• --start-pend — starting pendant branch length. Default is 0.1. 🌱
• --max-pend — set the maximum ML pendant branch length. Default is 2. 🚧
• --fig-cutoff — the cutoff for determining figs. Default is 0; specify 0 to disable. 🍑
• --fig-eval-all — evaluate all likelihoods to make sure the best location was actually selected. no shortcuts, no regrets. 🔍
• --fig-eval-discrepancy-tree — write out a tree showing the discrepancies between the best complete and observed locations. 🌲
• --fig-tree — write out a tree showing the figs on the tree. 🌴
• --max-strikes — maximum number of strikes for baseball. 0 -> no ball playing. Default is 6. ⚾
• --strike-box — set the size of the strike box in log likelihood units. Default is 3. 📦
• --max-pitches — set the maximum number of pitches for baseball. Default is 40. 🥎
• --fantasy — desired likelihood cutoff for fantasy baseball mode. 0 -> no fantasy. 🏟️
• --fantasy-frac — fraction of fragments to use when running fantasy baseball. Default is 0.1. 🎢
• --write-masked — write the alignment masked to the region without gaps in the query. 🎭
• --verbosity — set verbosity level. 0 is silent, and 2 is quite a lot. Default is 1. 🔊
• --out-dir — specify the directory to write place files to. 📂
• -o — specify the output file name. 📝
• --pretend — only check out the files then report. Do not run the analysis. 🙈
• --check-like — write out the likelihood of the reference tree, calculated two ways. 🔁
• -j — the number of child processes to spawn when doing placements. Default is 2. 👯
• --timing — display timing information after the pplacer run finishes. ⏱️
• --no-pre-mask — don't pre-mask sequences before placement. 🚫
• --write-pre-masked — write out the pre-masked sequences to the specified fasta file before placement. 🗂️
• --map-mrca — specify a file to write out MAP sequences for MRCAs and corresponding placements. 🧭
• --map-mrca-min — specify cutoff for inclusion in the MAP sequence file. Default is 0.8. ✂️
• --map-identity — add the percent identity of the query sequence to the nearest MAP sequence to each placement. 💯
• --keep-at-most — the maximum number of placements we keep. Default is 7. 🤲
• --keep-factor — throw away anything that has ml_ratio below keep_factor times (best ml_ratio). Default is 0.01. 🗑️
• --mrca-class — classify with MRCAs instead of a painted tree. 🎨
• --groups — split the query alignment into the specified number of groups. 🧩
• --always-refine — always refine the model before placing. glow-up first, always. ✨
• --mmap-file — instead of doing large allocations, mmap the given file. It will be created if it doesn't exist. 🗺️
• --discard-nonoverlapped — when pre-masking, silently discard sequences which don't overlap the mask. 🤫
• --version — write out the version number and exit. 🏷️
• -help — display this list of options. 🙋
• --help — display this list of options. 🙋

lowkey important: --pretend means she does not run the analysis. she just checks the files out and reports. don't be surprised when nothing gets placed, bestie. 😭

🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole thing, fr fr. pplacer 1.1~alpha19, June 2020 — go place some reads, you've got this. 💜🌈🧚