RUN-SEPP.SH(1)

💖 NAME 💖

okay bestie, say hi to run-sepp.sh — a phylogenetic placement tool ✨ no cap, that's literally what it is.

🌸 DESCRIPTION 🌸

here's the vibe — this is how you run it:

run-sepp.sh [input fragments file] [output prefix] [-x N] [-A ALIGN] [-P N] [any other SEPP argument] [-t TREE] [-a ALIGN] [-r RAXML] [-n argN] [-b argB]

like, that's the whole shape of it. input fragments file first, output prefix second, and then all the little knobs and dials after 🎀

✨ OPTIONS ✨

• -x N, --cpu N — use N cpus. [default: however many cpus your machine has available — it just takes what's there 🫶]
• -A ALIGN, --alignmentSize ALIGN — the max alignment subset size, set to ALIGN. [default: 10% of the total number of taxa, OR the placement subset size if one was given 👑]
• -P N, --placementSize N — the max placement subset size, set to N. [default: 10% of the total number of taxa, OR the alignment length — whichever one is bigger 🦋]
• -t TREE, --referencePhylogeny TREE — your input tree file, newick format only. [default: None 😭]
• -a ALIGN, --referenceAlignment ALIGN — an aligned fasta file. [default: None 🙈]
• -r RAXML, --referenceInfoFile RAXML — a RAxML_info file holding the model parameters, generated by RAxML. [default: None]
• -n argN, --noTreeComputation argN — if you set this to something (like, say, 1), then no tree computation happens at all — it's just the placements one. that's it. that's the whole thing 💅
• -b argB, --debugInformation argB — if you set this to something (again, 1 works), it reports debugging information. very "tell me everything" of it 🍓

optional commands do NOT need to be in any particular order, bestie — order is not the moment. and any SEPP option can be passed through too. for example, -x 8 makes SEPP use 8 threads ⭐

🌈 SEE ALSO 🌈

run_sepp.py(5) — go read that one too, iykyk 💜

mwah, that's the page 🎀 this was run-sepp.sh, from September 2021, sitting in the User Commands section as RUN-SEPP.SH(1) — iconic, timeless, periodt. 💖✨