bali-phy(1)

📦
version 4.1 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 bali-phy — Bayesian Inference of Alignment and Phylogeny 💖

okay bestie, sit down, hydrate, because this is the bali-phy(1) manual page and it's genuinely iconic. it's giving "my best friend is a phylogenetics tool and she ate". let's get into it 🧚✨

🌸 NAME 🌸

bali-phy — Bayesian Inference of Alignment and Phylogeny. no cap, that's literally her whole job description.

✨ SYNOPSIS ✨

bali-phy sequence-file1 [sequence-file2 ...]  [OPTIONS]

bali-phy help topic

like, you feed her sequence files and options, or you ask her for help on a topic. that's the whole vibe. 💅

🦋 DESCRIPTION 🦋

so bali-phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. she uses MCMC and Bayesian methods to estimate evolutionary trees, positive selection, and branch lengths while averaging over alternative alignments. the way she just... averages over the alignments? obsessed. 🔥

BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes and BEAST) using substitution models like GTR+gamma. and she automatically estimates relative rates for each gene. main character energy fr fr 👑

🎀 GENERAL OPTIONS 🎀

for each option below, more info is available by specifying the long form of the option as a help topic. for example: bali-phy help alphabet. iykyk 💜

  • -h, --help, --help=topic — display a friendly help message. specify --help=advanced or --help=expert to display more advanced options. (yes she has layers bestie)
  • -v, --version — print version information. a little "who am i" moment ⭐
  • -V, --verbose, --verbose NUM — print extra output to aid in trouble-shooting. if NUM is not specified the default is 1. values from 2 to 4 increase the amount of information displayed.
  • -t, --test — analyze the initial values and exit. lil vibe check, then she's out 🙈
  • -c filename, --config filename — read commands from filename before command line.

🔥 MCMC OPTIONS 🔥

  • -i NUM, --iterations NUM — the number of iterations to run.
  • -n STRING, --name STRING — name for the output directory to create.
  • -x NUM, --subsample NUM — factor by which to subsample. > this option should usually not be used. so like... don't? 😭
  • -s NUM, --seed NUM — random seed. useful for replaying specific runs when trouble-shooting.
  • -l arg, --log-format arg — log-format: tsv or json or tsv,json.

🌈 PARAMETER OPTIONS 🌈

  • -T filename, --tree filename — file with initial tree in Newick format or NEXUS format.
  • -U, --unalign — unalign all variable-alignment partitions before starting MCMC instead using the supplied alignment as a starting value.

👑 MODEL OPTIONS 👑

  • -A alphabet, --alphabet alphabet — the alphabet.
  • -S model, --smodel model — the substitution model.
  • -I model, --imodel model — the insertion-deletion model.
  • -R arg, --scale arg — prior on the scale.
  • -F arg, --fix arg — fix topology, tree, or alignment
  • -L NUMS, --link NUMS — link partitions. takes a comma-separated list of numbers indicating partitions. for example --link 1,2,3.
  • --variables arg — variable definitions

💜 EXAMPLES 💜

  1. analyze sequences in dna.fasta under the GTR model:
bali-phy dna.fasta --smodel gtr
  1. perform a traditional fixed-alignment analysis with gaps treated as missing data:
bali-phy dna.fasta -S gtr -I none
  1. perform an analysis of 3 genes where each gene has a different substitution mode — and the sequence names in all three files must be the same, bestie, don't forget 😭:
bali-phy dna.fasta amino.fasta codons.fasta -S 1:gtr -S 2:lg08 -S 3:gy94

🍓 REPORTING BUGS 🍓

BAli-Phy online help: http://www.bali-phy.org/docs.php.

please send bug reports to bali-phy-users@googlegroups.com. she wants to hear from you 🫶

⭐ SEE ALSO ⭐

bp-analyze

🌸 AUTHORS 🌸

Benjamin Redelings.

and that's the whole page bestie 💅 this one's dated Nov 2024, it's part of the bali-phy(1) manual, so go forth and infer some phylogenies. slay, periodt, bye 🎀✨

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