PhyML(1)

💖 NAME 💖

phyml, phyml-mpi — phylogeny estimation using Maximum Likelihood ✨

🦋 SYNOPSIS 🦋

phyml [command args]

okay so bestie, every single option below is optional — except -i, and only if you actually wanna use the command-line interface. that's it, that's the rule 💅

🎀 Command options 🎀

• -i (or --input) seq_file_name — seq_file_name is the name of your nucleotide or amino-acid sequence file, and it has to be in PHYLIP format. no PHYLIP, no party 🙈
• -d (or --datatype) data_type — data_type is nt for nucleotide (that's the default bestie), aa for amino-acid sequences, or generic — and for generic you use the NEXUS file format plus the symbols parameter here. iykyk 🧚
• -q (or --sequential) — flips the format from interleaved (which is the default) over to sequential. that's the whole vibe shift 💫
• -n (or --multiple) nb_data_sets — nb_data_sets is an integer, and it's literally just how many data sets you wanna analyse. 🍓
• -p (or --pars) [] — use a minimum parsimony starting tree. this one only counts when the -u option is absent and when tree topology modifications are to be done. 👑
• -b (or --bootstrap) int — the bootstrap brain, and it does so many different things depending on the number you feed it:
  • int > 0: int is the number of bootstrap replicates.
  • int = 0: neither approximate likelihood ratio test nor bootstrap values are computed.
  • int = -1: approximate likelihood ratio test returning aLRT statistics.
  • int = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.
  • int = -4: (default) SH-like branch supports alone.
• -m (or --model) model — model is the substitution model name, and there are two whole menus:
  • Nucleotide-based models: HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom
    • for the custom option, a string of six digits identifies the model. For instance, 000000 corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform). 012345 corresponds to GTR. This option can be used for encoding any model that is nested within GTR.
  • Amino-acid based models: LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT Blosum62 | MtMam | MtArt | HIVw | HIVb | custom
• --aa_rate_file filename — filename is the name of the file that provides the amino acid substitution rate matrix in PAML format. and bestie, it is compulsory to use this option when analysing amino acid sequences with the custom model. no file, no custom, periodt 🚫
• -f e, m, or fA,fC,fG,fT — the character frequencies option, and each mode hits different:
  • e : the character frequencies are determined as follows :
    • Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting the occurrence of the different bases in the alignment.
    • Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting the occurrence of the different amino-acids in the alignment.
  • m : the character frequencies are determined as follows :
    • Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood.
    • Amino-acid sequences: (Model) the equilibrium amino-acid frequencies are estimated using the frequencies defined by the substitution model.
  • "fA,fC,fG,fT" : only valid for nucleotide-based models. fA, fC, fG and fT are floating numbers that correspond to the frequencies of A, C, G and T respectively.

⚠️ WARNING bestie: do not use any blank space between your values of nucleotide frequencies, only commas! not even one little space. i'm serious. 😭

• -t (or --ts/tv) ts/tv_ratio — ts/tv_ratio is the transition/transversion ratio. DNA sequences only. it can be a fixed positive value (ex: 4.0) or e to get the maximum likelihood estimate. 🌸
• -v (or --pinv) prop_invar — prop_invar is the proportion of invariable sites. it can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. 🎀
• -c (or --nclasses) nb_subst_cat — nb_subst_cat is the number of relative substitution rate categories. Default: nb_subst_cat=4. Must be a positive integer. 💜
• -a (or --alpha) gamma — gamma is the distribution of the gamma distribution shape parameter. can be a fixed positive value or e to get the maximum likelihood estimate. ✨
• -s (or --search) move — the tree topology search operation option. it can be either NNI (default, fast), or SPR (a bit slower than NNI), or BEST (best of NNI and SPR search). choose your fighter 👑
• -u (or --inputtree) user_tree_file — user_tree_file is the starting tree filename. the tree must be in Newick format. 📐
• -o params — this option focuses on specific parameter optimisation. the menu goes like this:
  • params=tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
  • params=tl : tree topology and branch length are optimised.
  • params=lr : branch length and rate parameters are optimised.
  • params=l : branch length are optimised.
  • params=r : rate parameters are optimised.
  • params=n : no parameter is optimised.
• --rand_start — this option sets the initial tree to random. it is only valid if SPR searches are to be performed. 🎲
• --n_rand_starts num — num is the number of initial random trees to be used. it is only valid if SPR searches are to be performed. 🌈
• --r_seed num — num is the seed used to initiate the random number generator. Must be an integer. 🎰
• --print_site_lnl — print the likelihood for each site in file *_phyml_lk.txt. 🍓
• --print_trace — print each phylogeny explored during the tree search process in file *_phyml_trace.txt. 🔍
• --run_id ID_string — append the string ID_string at the end of each PhyML output file. this option may be useful when running simulations involving PhyML. 💅
• --quiet — no interactive question (for running in batch mode) and quiet output. shhh 🤫
• --no_memory_check — no interactive question for memory usage (for running in batch mode). normal output otherwise. 🧠
• --alias_subpatt — site aliasing is generalized at the subtree level. sometimes leads to faster calculations. See Kosakovsky Pond SL, Muse SV, Systematic Biology (2004) for an example. ⚡
• --boot_progress_display num (default=20) — num is the frequency at which the bootstrap progress bar will be updated. Must be an integer. 📊

🫶 PHYLIP-LIKE INTERFACE 🫶

you can also run PhyML with no argument at all, bestie — in that case you change the value of a parameter by typing its corresponding character as shown on screen. interactive icon behaviour, honestly 😌

✨ EXAMPLES ✨

DNA interleaved sequence file, default parameters:

phyml -i seqs1

AA interleaved sequence file, default parameters:

phyml -i seqs2 -d aa

AA sequential sequence file, with customization:

phyml -i seqs3 -q -d aa -m JTT -c 4 -a e

🌸 SEE ALSO 🌸

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

Stephane Guindon and Olivier Gascuel, Systematic Biology 52(5):696-704, 2003.

please cite this paper if you use this software in your publications. fr fr, it's the polite thing to do 🫶

👑 AUTHOR 👑

PhyML was written by Stephane Guindon and Olivier Gascuel and others.

This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (but may be used by others).

and that's the whole page, bestie 💖 this was phyml version 3.0, living in the PhyML(1) slot of the User Commands manual. go estimate some trees, you absolute main character 🌈👑✨