EXAML(1)

👑 EXAML — the manual page, but make it make sense 💅

okay bestie, sit down, hydrate, because we're talking about EXAML — Exascale Maximum Likelihood (ExaML) code for phylogenetic inference. 🦋 And it's not just one binary, it's a whole squad: there's examl, and then examl-AVX (same thing but using AVX ✨), and examl-OMP (same thing but using OMP ✨), and examl-OMP-AVX (the overachiever — AVX and OMP together, main character energy fr). Four icons, one manpage, we love to see it. 💖

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🌸 SYNOPSIS 🌸

examl|examl-AVX|examl-OMP|examl-OMP-AVX -s binarySequenceFileName -n
outputFileNames -m rateHeterogeneityModel -t userStartingTree|-R
binaryCheckpointFile|-g constraintTree -p randomNumberSeed [-np NP] [-a]
[-B numberOfMLtreesToSave] [-c numberOfCategories] [-D] [-e
likelihoodEpsilon] [-f d|e|E|o|q] [-h] [-i initialRearrangementSetting]
[-I quartetCheckpointInterval] [-M] [-r randomQuartetNumber] [-S] [-v]
[-w outputDirectory] [-Y quartetGroupingFileName]
[--auto-prot=ml|bic|aic|aicc]

that's the whole vibe in one block, no cap. 🫶

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✨ OPTIONS ✨

so here's every single flag, and yes, we're doing all of them. no skipping, that's not the energy today. 💜

• -np NP — NP is the number of processors to use for MPI. If you don't specify it, some hopefully sensible guess gets made. 🔮 Heads up: this one is a specific option of the Debian wrapper in /usr/bin. so like, it's the Debian-specific bestie, not the upstream one. 🎀
• -a — use the median for the discrete approximation of the GAMMA model of rate heterogeneity.

DEFAULT: OFF

• -B — specify the number of best ML trees to save and print to file. 🌈
• -c — Specify number of distinct rate catgories for ExaML when modelOfEvolution is set to GTRPSR. Individual per-site rates are categorized into numberOfCategories rate categories to accelerate computations. (yes it says "catgories" in the original, we're keeping it, iconic typo, no notes 💀)

DEFAULT: 25

• -D — ML search convergence criterion. This will break off ML searches if the relative Robinson-Foulds distance between the trees obtained from two consecutive lazy SPR cycles is smaller or equal to 1%. Usage recommended for very large datasets in terms of taxa. On trees with more than 500 taxa this will yield execution time improvements of approximately 50% while yielding only slightly worse trees. so basically: speed for a tiny bit of tree quality, your call bestie. ⚖️

DEFAULT: OFF

• -e — set model optimization precision in log likelihood units for final optimization of model parameters.

DEFAULT: 0.1

• -f — select algorithm. okay this one has layers, let's go 🧚:

"-f d": new rapid hill-climbing DEFAULT: ON

"-f e": compute the likelihood of a bunch of trees passed via -t

this option will do a quick and dirty optimization without re-optimizng the model parameters for each tree. (again — original spelling, keeping it fr 💅)

"-f E": compute the likelihood of a bunch of trees passed via -t

this option will do a thorough optimization that re-optimizes the model parameters for each tree. ✨ the careful one.

"-f o": old and slower rapid hill-climbing without heuristic cutoff. it's giving vintage.

"-f q": fast quartet calculator

DEFAULT for "-f": new rapid hill climbing

• -g — Pass a multi-furcating constraint tree to ExaML. The tree needs to contain all taxa of the alignment! ⚠️ When using this option you also need to specify a random number seed via "-p". don't forget the seed, she will not run without it.
• -h — Display this help message. your little emergency button. 🆘
• -i — Initial rearrangement setting for the subsequent application of topological changes phase.
• -I — Set after how many quartet evaluations a new checkpoint will be printed.

DEFAULT: 1000

• -m — Model of rate heterogeneity 🌈

select "-m PSR" for the per-site rate category model (this used to be called CAT in RAxML). select "-m GAMMA" for the gamma model of rate heterogeneity with 4 discrete rates.

• -M — Switch on estimation of individual per-partition branch lengths. Only has effect when used in combination with "-q". Branch lengths for individual partitions will be printed to separate files. A weighted average of the branch lengths is computed by using the respective partition lengths. 🎀

DEFAULT: OFF

• -n — Specifies the name of the output file.
• -p — Specify a random number seed, required in conjunction with the "-g" option for constraint trees. 🔑
• -R — read in a binary checkpoint file called ExaML_binaryCheckpoint.RUN_ID_number. your save file, your comeback arc. 💾
• -r — Pass the number of quartets to randomly sub-sample from the possible number of quartets for the given taxon set. Only works in combination with -f q ! 🚨
• -s — Specify the name of the BINARY alignment data file generated by the parser component.
• -S — turn on memory saving option for gappy multi-gene alignments. For large and gappy datasets specify -S to save memory. This will produce slightly different likelihood values, may be a bit slower but can reduce memory consumption from 70GB to 19GB on very large and gappy datasets. 📉 seventy gigs down to nineteen, that's the glow-up.
• -t — Specify a user starting tree file name in Newick format. 🌳
• -v — Display version information.
• -w — FULL (!) path to the directory into which ExaML shall write its output files. like the FULL path, bestie, not a vibe, an actual path. 📁

DEFAULT: current directory

• -Y — Pass a quartet grouping file name defining four groups from which to draw quartets. The file input format must contain 4 groups in the following form: (Chicken, Human, Loach), (Cow, Carp), (Mouse, Rat, Seal), (Whale, Frog); Only works in combination with -f q ! 🐔🐄🐭🐋
• --auto-prot=ml|bic|aic|aicc — When using automatic protein model selection you can chose the criterion for selecting these models.

RAxML will test all available prot subst. models except for LG4M, LG4X and GTR-based models, with and without empirical base frequencies. You can chose between ML score based selection and the BIC, AIC, and AICc criteria.

DEFAULT: ml

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🫶 AUTHOR 🫶

Alexandros Stamatakis, Andre J. Aberer, and Alexey Kozlov on February 14 2017. (valentine's day release, romantic honestly 💌)

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🎀

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and that's the whole thing, bestie. this page came from examl version 3.0.18, dated February 2017 — so go forth, run your phylo thing, and slay. 👑✨ bye!! 💖