RATE4SITE(1)

💖 RATE4SITE(1) 💖

User Commands · rate4site · ok bestie sit down we're doing phylogenetics today 🧬✨

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🌸 NAME 🌸

rate4site — the detector of conserved amino-acid sites 👑

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✨ SYNOPSIS ✨

rate4site [OPTIONS] -s <MSA FILE>

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🦋 DESCRIPTION 🦋

Okay so here's the tea: the rate of evolution is not constant among amino acid sites. Some positions evolve super slowly and we call those "conserved", and some evolve fast and we call those "variable". The way the rate varies corresponds to different levels of purifying selection acting on these sites. And purifying selection can come from like, so many places: geometrical constraints on how the protein folds into its 3D structure, constraints at amino acid sites that are involved in enzymatic activity or in ligand binding, or alternatively at amino acid sites that take part in protein-protein interactions.

So rate4site calculates the relative evolutionary rate at each site using a probabilistic-based evolutionary model. Which is iconic of it because it lets you take into account the stochastic process underlying sequence evolution within protein families and the phylogenetic tree of the proteins in the family. And the conservation score at a site? That's literally just the site's evolutionary rate. 💅

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🔬 METHODOLOGY 🔬

The sole obligatory input to Rate4Site is an MSA file. Then the program computes a phylogenetic tree that's consistent with the available MSA (tho bestie, you can also input a pre-calculated tree if you want, we support you). Then it calculates the relative conservation score for each site in the MSA. This gets carried out using either an empirical Bayesian method or a maximum likelihood method (Pupko et al., 2002). The differences between the two methods are explained in details in Mayrose et al (2004). no cap.

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📚 REFERENCES 📚

Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004. Comparison of site-specific rate-inference methods: Bayesian methods are superior. Mol Biol Evol 21: 1781-1791.

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💅 OPTIONS 💅

• -s MSA_FILE — The input sequence file name. The following formats are supported: Mase, Molphy, Phylip, Clustal, Fasta
• -t — The input tree file name (in Newick format)
• -o OUTPUT_FILE — The results output file
• -a — Reference sequence name in the MSA. The conservation scores are printed based on the amino-acids in this sequence.
• -k — The number of discrete Gamma categories
• -m — Evolutionary model. The following amino-acids models are supported:

DAY (-md), JTT (-mj), REV (-mr), aaJC (-ma), LG (-Ml), WAG (-Mw) .

For nucleotides, the following models are supported: JC (-mn), HKY (-Mh), Tamura92 (-Mt), GTR (-Mg).

• -b — Branch lengths optimization flag:
  • -bn = no Branch lengths optimization
  • -bh = optimization using a homogeneous model (no among-site-rate-variation)
  • -bg = optimization using a Gamma model
• -i — Rate inference method flag:
  • -Im = rates are inferred using the maximum likelihood method
  • -Ib = rates are inferred using the empirical Bayes method
• -z — Tree constructing method
  • zj = Neighbor-joining tree with Jukes-Cantor distances
  • zn = Neighbor-joining tree with maximum likelihood distances
• -h — Short help message

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👑 AUTHOR 👑

Nir Ben-Tal <NirB@tauex.tau.ac.il> 💌

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🌈 SEE ALSO 🌈

Main website

<http://www.tau.ac.il/~itaymay/cp/rate4site.html>

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and that's the whole page bestie, you're so ready for your MSA era 🧚‍♀️🦋💖

version 3.0.0 · dated 2022-01-20 · mwah, go conserve some sites 💅✨🎀