extract-ancestors(1)

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

💖 extract-ancestors(1) 💖

okay bestie, gather round, because this is the extract-ancestors page from section 1 of the manual, and it's lowkey one of the most useful little gremlins in the whole toolchain. sit with me. 🫶

✨ NAME ✨

extract-ancestors — Extract and name ancestral sequences according to node- and branch- queries. 🧬

✨ SYNOPSIS ✨

extract-ancestors [OPTIONS]

like, that's it. no positional args. all vibes, all options. 💅

✨ DESCRIPTION ✨

Extract and name ancestral sequences according to node- and branch- queries.

fr fr, that's the whole pitch: you hand it a query, it goes and finds the ancestral sequences that match, and it names them for you. main character energy. 👑

✨ GENERAL OPTIONS ✨

  • -h, --help — produces help message. the classic. when in doubt, ask for help. 🙈
  • -V, --verbose [=arg(=1)] — Show more log messages on stderr. so if you're nosy (respect) you can crank up the chatter. 🗣️

✨ INPUT OPTIONS ✨

  • -A arg, --alignments arg — File of alignment samples. this is your alignment file, bestie. 🍓
  • -T arg, --trees arg — File of corresponding tree samples. and this is the tree file that matches it. they're a set, they go together. 🦋
  • -x arg (=10), --subsample arg (=10) — factor by which to sub-sample trees. default is 10, so unless you say otherwise it's sub-sampling every 10th tree. ✨

✨ ANCESTOR QUERY OPTIONS ✨

  • -n arg, --nodes arg — Newick tree with labelled ancestors. give it a Newick tree and label the ancestors in it, that's your query. 🌳
  • -g arg, --groups arg — File with named groups. want to query by group instead? here's where the named groups live. 🎀
  • --nodes-min arg (=0.34) — Minimum fraction to include a node. default 0.34. if a node doesn't clear that bar, it's not making the cut. 💀
  • --groups-min arg (=0.34) — Minimum fraction to include a group. same deal, default 0.34, but for groups. 🫶

✨ EXAMPLES ✨

Add named ancestral sequences to alignments where they are present:

% extract-ancestors -A C1.P1.fastas -T C1.trees --nodes query.tree --groups query.tree

see how it's passing --nodes query.tree AND --groups query.tree? yeah. iconic. 🌈

✨ REPORTING BUGS ✨

found a bug? don't just scream into the void, tell the people who can fix it. 💌

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

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

✨ AUTHORS ✨

Benjamin Redelings. 👑

and that's the whole page, babe. this version came from the extract-ancestors(1) page dated Feb 2018. go forth and extract some ancestors, you've got this. 💖✨🎀

📦 where this page comes from