GARLI(1)

💖 GARLI(1) 💖

okay bestie, sit down, hydrate, because we're about to talk about garli — that's the MPI version of the whole situation, in case the manual page name at the top wasn't giving it away 💅

✨ NAME ✨

garli — phylogenetic analysis of molecular sequence data using maximum-likelihood (MPI version) 🌳🧬

🌈 SYNOPSIS 🌈

mpirun [MPI OPTIONS] garli-mpi -[# of times to execute config file]
[config filename]

like... that's the whole summoning ritual, no cap 🔮

🦋 DESCRIPTION 🦋

so GARLI stands for Genetic Algorithm for Rapid Likelihood Inference (yes the acronym ate, we love an acronym that eats) and it's a program for inferring phylogenetic trees 🌲🌲🌲

the way it works is it uses an approach similar to a classical genetic algorithm to rapidly search the space of evolutionary trees and model parameters until it finds the solution that maximizes the likelihood score. it's literally evolution doing evolution. main character energy fr fr 👑

it implements nucleotide, amino acid and codon-based models of sequence evolution, and it runs on all platforms — she's versatile, she's everywhere, she's booked and busy 💅

the latest version adds support for partitioned models and morphology-like datatypes 🦴✨

and just so we're clear bestie: this is the MPI version of Garli. not the regular one. the parallel one. she's got friends 🫶

🎀 OPTIONS 🎀

• -i, --interactive — interactive mode, aka it will allow and/or expect user feedback from you. it wants to chat. it wants your input. respect it 💬
• -b, --batch — batch mode, aka do not expect user input, it's gonna do its thing solo. (also batch is the default for the version you are running, so if you didn't pick anything, congrats, you picked this 🎉)
• -v, --version — print version information and dip. that's it, that's the whole job ✌️
• -h, --help — print this help and exit. your little emergency exit door 🚪
• -t — run internal tests (heads up: this requires dataset and config file, so don't come empty-handed bestie 🙈)
• -V — validate: load config file and data, validate config file, data, starting trees and constraint files, print required memory and selected model, then exit. like a lil pre-flight checklist for your tree ✈️✅

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 name your file right or she's gonna be searching the wrong room 😭

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. king behavior honestly 🫶

and that's the whole page bestie, you're officially GARLI-pilled 🧚💜

this was garli 2.1, dated June 2016, filed under GARLI(1) — mwah, go build a tree 💅🌸