summarize-ancestors(1)

📦
version 4.1 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 summarize-ancestors(1) 💖

okay bestie, so this is the manual page for summarize-ancestors — yes it's a mouthful, yes it eats, we move 💅

✨ NAME ✨

summarize-ancestors — constructs alignments with internal sequences for labeled nodes in the query tree. it's giving "fill in the blanks but the blanks are your ancestors" 🧬

🌸 SYNOPSIS 🌸

summarize-ancestors alignment -A fastas1 -T trees1 [OPTIONS]

🦋 DESCRIPTION 🦋

Construct alignments with internal sequences for labeled nodes in query tree. that's the whole bit — you got a query tree, you got labeled nodes, and this thing builds you alignments that include the internal sequences for those nodes. iconic behaviour, fr fr ✨

👑 GENERAL OPTIONS 👑

  • -h, --help — produces help message. when in doubt, ask for help, no shame in it 🫶
  • -V, --verbose — [=arg(=1)] Show more log messages on stderr. more logs = more lore, and it all goes to stderr 💬

🎀 INPUT OPTIONS 🎀

  • -A arg, --alignments arg — File of alignment samples. this is your alignment file, hand it over 🍓
  • -T arg, --trees arg — File of corresponding tree samples. and here's the matching tree file — they're a set, don't split them up 😭
  • -x arg (=10), --subsample arg (=10) — factor by which to sub-sample trees. defaults to 10. thinning the tree herd, periodt 🌈
  • -m arg (=500), --max arg (=500) — Thin (alignment,tree) pairs down to this number of samples. defaults to 500. yes bestie, we're capping the pairs, main character energy only 👑

🧚 ANCESTOR QUERY OPTIONS 🧚

  • -n arg, --nodes arg — Newick tree with labelled ancestors. newick format, ancestors labelled, chef's kiss 💜
  • -g arg, --groups arg — File with named groups. groups, but named 📁
  • --nodes-min arg (=0.34) — Minimum fraction to include a node. defaults to 0.34. below that threshold? not invited to the party 💀
  • --groups-min arg (=0.34) — Minimum fraction to include a group. also defaults to 0.34. same energy, different noun 🌸

⭐ EXAMPLES ⭐

Add ancestral sequences to summary alignment:

% summarize-ancestors summary.fasta -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree

look at that one-liner. absolutely ate 🔥

🐛 REPORTING BUGS 🐛

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

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

found a bug? don't suffer in silence, bestie — email the list 💌

💜 AUTHORS 💜

Benjamin Redelings. yes, THE Benjamin Redelings 👑

heads up: the source/version line on this one says BAli-Phy and the date is Feb 2018, so if you're citing it or checking freshness — that's the tea 🫖

stay slay, go summarize those ancestors 💖✨🎀🦋🌸

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