GARLI(1)

📦 version 2.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 GARLI — like, the whole manual but make it make sense 💖

okay bestie, welcome to the manual for garli(1) — a User Commands situation, she's a classic. come sit with me, we're gonna read this together and you're gonna be obsessed. 🫶

✨ NAME ✨

garli — phylogenetic analysis of molecular sequence data using maximum-likelihood

no cap, that's the whole vibe. she infers trees. 💅

🌸 SYNOPSIS 🌸

garli [OPTION] [config filename]

like, you give her some options, you give her a config file, she does her little thing. iconic.

🦋 DESCRIPTION 🦋

okay so. GARLI stands for Genetic Algorithm for Rapid Likelihood Inference, and she is literally a program for inferring phylogenetic trees. 🔥

the way she works? it's giving classical genetic algorithm energy. she rapidly searches the space of evolutionary trees and model parameters, hunting down the solution that maximizes the likelihood score. main character behavior, honestly.

she implements nucleotide, amino acid, and codon-based models of sequence evolution, and — slay — she runs on all platforms. 🌈

and the latest version? she adds support for partitioned models and morphology-like datatypes. we love growth. we love evolution. very on brand. ✨

🎀 OPTIONS 🎀

  • -i, --interactive — interactive mode: she'll allow and/or expect user feedback. she wants to talk to you. 👑
  • -b, --batch — batch mode: do not expect user input. heads up though, bestie — batch is the default for the version you are running. 💅
  • -v, --version — print version information and dip. exit. bye. 🦋
  • -h, --help — print this help and exit. the classic. 🌸
  • -t — run internal tests. (requires dataset and config file — no skipping steps, babe 😭)
  • -V — validate: load config file and data, validate config file, data, starting trees and constraint files, print required memory and selected model, then exit. a full vibe check on your files. ✅
NOTE: If no config filename is passed on the command line the program will look in the current directory for a file named garli.conf. so if you're like "why is she not reading my config" — check your cwd, bestie, she's looking for garli.conf right there. 🙈

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. thank you Andreas, we appreciate you fr fr. 🫶

and that's the whole thing, bestie!! ✨ this was garli 2.1, dated June 2016, and yes she is still that girl — GARLI(1) forever. go infer some trees, you've got this. 💖🌷🧚‍♀️

📦 where this page comes from