TREEGEN(1)

✨ NAME ✨

okay bestie, say hi to treeGen — the User Commands icon living in TREEGEN(1) — and the NAME line is serving:

• treeGen — Enumerate rooted tree topologies, subject to constraints on

yes, it stops right there, cliffhanger energy, but the DESCRIPTION picks it up, no cap.

💖 DESCRIPTION 💖

Enumerate rooted tree topologies, subject to constraints on monophyletic groups. An outgroup is assumed to be specified. periodt 💅

🌈 SYNOPSIS 🌈

the main character usage is literally:

       treeGen spec1,spec2,spec3,... [group1,group2,...] > outfile OR

              treeGen '*speciesFile' ['*groupFile'] > outfile

(where speciesFile/groupFile contain whitespace-delimited names) The last species listed is assumed to be the outgroup. 🦋

The optional "groups" classification can be used to define monophyletic groups. Each species may be assigned a nonnegative integer indicating its group, with 0 indicating no group assignment. The integers should appear in the same order as the species names. For example,

treeGen human,chimp,macaque,mouse,rat,dog,horse,fugu
1,1,1,2,2,0,0,0

could be used to generate all topologies of the specified vertebrate species such that the primates (human, chimp, and macaque) and the rodents (mouse and rat) appear as monophyletic groups. The outgroup should always be assigned a group of 0 (a nonzero value will be ignored). 👑

🎀 OPTIONS 🎀

the options section is a short king, just one flag, and it's iconic:

• --help, -h — Print this help message.

and that's the page, bestie 💖 this was treeGen 1.4, May 2016, serving TREEGEN(1) energy. slay ✨