primeGEM(1)

💖 primeGEM(1) — the guest-in-host tree reconciliation bestie 💖

okay so picture this: you've got a guest tree and a species tree and they are NOT vibing yet, and primeGEM is the friend who sits them both down and does the guest-in-host tree reconciliation. that's literally the whole job. it's giving matchmaker energy, fr fr. 🧚✨

this page lives in the General Commands Manual section, section 1, iykyk.

✨ SYNOPSIS ✨

primeGEM [OPTIONS] guest-tree species-tree [gene-species-map]

like yes bestie, three positional things, the last one's optional, we love a flexible queen 💅

🌸 DESCRIPTION 🌸

so here's who's who in this little ensemble:

• guest-tree — the name of the file containing the guest tree. that's it, that's the file. 🎀
• species-tree — the species tree, in Newick format, with divergence times. no cap, you need the divergence times, don't show up without them.
• gene-species-map — a file where every line has a gene name chillin' in the first column and a species name in the second, and that species name has to be one that's actually in the species tree. alternatively? you can also choose to associate the genes with species in the gene tree instead. your call, main character. 🦋

👑 OPTIONS 👑

every single one, in order, no skips, because we do NOT gatekeep here:

• -h, -u — display help (this text). hi bestie, you're reading it 🫶
• -o FILE — output filename. name your baby.
• -i INT — number of iterations.
• -t INT — thinning.
• -m — do maximum likelihood. no MCMC. straight to the point, no walking around the block.
• -w INT — write to stderr INT times less often than to stdout.
• -s INT — seed for the pseudo-random number generator. if you set it to 0 (which is the default), the process id gets used as the seed instead. so if you want reproducible vibes, set a real number, okay? 😭
• -q — do not output diagnostics to stderr. quiet. shy. mysterious. 🙈
• -g — debug info. for when you need to see everything, and i mean everything.
• -l — output likelihood. no MCMC.
• -Gr — reroot gene tree. the default is a fixed root, so this is you switching it up.
• -Go — estimate orthology. the default is to discard orthology data, so again, you're the one making moves.
• -Gs — record speciation probabilities. heads up bestie: orthology probabilities will not be recorded when you do this. it's one or the other, pick your fave. ⭐
• -Bf FLOAT FLOAT — fix the birth/death rates to these values.
• -Bp FLOAT FLOAT — start values of birth/death rate parameters.
• -Bt FLOAT — fix 'top time', the time between the first duplication and root of S, to this value.
• -Bb FLOAT — the beta parameter for a prior distribution on species root distance.

💀 EXIT STATUS 💀

• 0 — successful program execution. slay. ✨
• 1 — some error occurred. not slay. 😭

🌈 URL 🌈

the prime-phylo home page: http://prime.sbc.su.se

(go say hi, it's iconic.)

🎀 SEE ALSO 🎀

your other faves, all linked up: primeDTLSR(1), primeDLRS(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)

okay that's the whole page, you're officially educated, go reconcile some trees 💜

this little love letter is from prime-phylo version 1.0.11, dated 13 Mar, 2012 — yeah she's an elder icon and we respect her. periodt. 👑🌸