RUN_SEPP.PY(1)

💖 run_sepp.py — a phylogenetic placement tool 💖

okay bestie, sit down, grab a boba, because we're about to talk about run_sepp.py, a User Commands girlie who lives in section 1 of your manual pages. she places stuff on trees. phylogenetically. it's giving ✨science✨ and honestly? she ate.

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🎀 NAME 🎀

run_sepp.py — a phylogenetic placement tool 🦋

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🌸 DESCRIPTION 🌸

so here's the whole vibe. you run her like this:

usage: run_sepp.py [-h] [-v] [-A N] [-P N] [-F N] [-D DISTANCE] [-M
DIAMETER]
       [-S DECOMP] [-p DIR] [-rt] [-o OUTPUT] [-d OUTPUT_DIR] [-c
CONFIG] [-t TREE] [-r RAXML] [-a ALIGN] [-f FRAG] [-m MOLECULE]
       [--ignore-overlap] [-x N] [-cp CHCK_FILE] [-cpi N] [-seed N]

and what she does — no cap — is run the SEPP algorithm on an input tree, an alignment, a fragment file, and a RAxML info file. that's the whole job. she's booked and busy 💅

optional arguments 💫

• -h, --help — shows this help message and dips. classic. 🙈
• -v, --version — shows the program's version number and exits. her little birth certificate. 👑

🧬 DECOMPOSITION OPTIONS 🧬

these ones decide the alignment decomposition size and the taxon insertion size. if you pass None, the default is to align/place at 10% of total taxa. also super important: the alignment decomosition size must be less than the taxon insertion size. like, mandatory. it's the rules. 😤

• -A N, --alignmentSize N — max alignment subset size of N. default is 10% of the total number of taxa or the placement subset size if given. ✨
• -P N, --placementSize N — max placement subset size of N. default is 10% of the total number of taxa or the alignment length (whichever bigger). she said whichever bigger, periodt. 💅
• -F N, --fragmentChunkSize N — maximum fragment chunk size of N. this one helps you control memory, so if your machine is struggling, she's your girl. default: 20000. 🫶
• -D DISTANCE, --distance DISTANCE — minimum p-distance before stopping the decomposition. default: 1. 🛑
• -M DIAMETER, --diameter DIAMETER — maximum tree diameter before stopping the decomposition. default: None. 🌳
• -S DECOMP, --decomp_strategy DECOMP — the decomposition strategy. default: using tree branch length. iconic behaviour honestly. 🌈

📤 OUTPUT OPTIONS 📤

these control the output. where the girlies go. 🎀

• -p DIR, --tempdir DIR — Tempfile files will be written to DIR. Full-path required. default: /tmp/sepp. don't be lazy with the path bestie. ⚠️
• -rt, --remtemp — Remove tempfile directory. default: disabled. she cleans up after herself when you ask nicely. 🧹
• -o OUTPUT, --output OUTPUT — output files with prefix OUTPUT. default: output. 💖
• -d OUTPUT_DIR, --outdir OUTPUT_DIR — output to the OUTPUT_DIR directory. full-path required. default: . 🗂️

📥 INPUT OPTIONS 📥

these control the input. and listen, to actually run SEPP the following is required, so no skipping:

• a backbone tree (newick format) 🌲
• a RAxML_info file — this is the file RAxML generates while estimating the backbone tree, and Pplacer uses this info file to set model parameters 🧠
• a backbone alignment file (fasta format) 📄
• a fasta file with the fragments 🧩

also heads up: the input sequences are assumed to be DNA unless you say otherwise. 🙈

• -c CONFIG, --config CONFIG — a config file with the options used to run SEPP. anything you pass as a command line argument overrides the config file value for that option. default: None. she respects your last word. 👑
• -t TREE, --tree TREE — input tree file (newick format). default: None. 🌳
• -r RAXML, --raxml RAXML — RAxML_info file including model parameters, generated by RAxML. default: None. 🤖
• -a ALIGN, --alignment ALIGN — aligned fasta file. default: None. 📑
• -f FRAG, --fragment FRAG — fragment file. default: None. 🧩
• -m MOLECULE, --molecule MOLECULE — molecule type of sequences. can be amino, dna, or rna. default: dna. choose your fighter. 💅
• --ignore-overlap — when a query sequence has the same name as a backbone sequence, ignore the query sequence and keep the backbone sequence. default: False. drama-free. ✌️

⭐ OTHER OPTIONS ⭐

these control how SEPP is run. the behind-the-scenes girlies. 🎬

• -x N, --cpu N — use N cpus. default: number of cpus available on the machine. she'll use everything she can get. 🔥
• -cp CHCK_FILE, --checkpoint CHCK_FILE — checkpoint file. default: no checkpointing. 😭
• -cpi N, --interval N — interval (in seconds) between checkpoint writes. has effect only with -cp provided. default: 3600. ⏰
• -seed N, --randomseed N — random seed number. default: 297834. keep her consistent bestie, reproducibility is a love language. 🎲

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👀 SEE ALSO 👀

sepp.config(5) — go read her too, she's part of the friend group 🫶

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that's the whole page bestie, go forth and place some taxa 💖✨

this was run_sepp.py, from the User Commands manual, dated Septbember 2020 — yes that's how it's spelled in the page and we love her for it, slay 💅