CONSENTROPY(1)

📦 version 1.8, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 NAME 💖

This is CONSENTROPY(1), a User Commands manual page for consEntropy. The NAME line itself is: consEntropy - For use with phastCons. Given phylogenetic models for conserved and (yep, it literally ends right there, bestie 😭)

✨ DESCRIPTION ✨

Okay so this tool is for use with phastCons, fr fr. Given phylogenetic models for conserved and non-conserved states, the target coverage, and the (prior) expected length of a conserved element, it computes all of this:

  • the relative entropy (H) of the phylogenetic models
  • the expected minimum number of conserved sites required to predict conserved element (L_min)
  • the "phylogenetic information threshold" (PIT = L_min * H)
  • the expected maximum number of nonconserved sites tolerated within a conserved element (L_max)

Also will make a recommendation for a new prior expected length based on a given target value of L_min*H (see --LminH). it's giving phylogenetics main character energy, no cap 🧚

🌸 SYNOPSIS 🌸

consEntropy [OPTIONS] <target-coverage> <expected-length> \

       [ <cons.mod> <noncons.mod> ]

💅 OPTIONS 💅

  • --H, -H <value> — Instead of computing the relative entropy from two .mod files, just use the specified value. The .mod files aren't required in this case. so if you already have the number, you can skip the mods bestie ✨
  • --LminH, -L <value> [or --NH/-N, for backward compatibility] — Report the expected length that would produce the specified value of L_min * H (i.e., the specified PIT), assuming H remains constant (it generally won't). Can be used iteratively to converge on a desired PIT. iykyk, it's the glow-up loop for your PIT 🦋
  • --help, -h — Print this help message. the classic "help me bestie" button 🫶

📝 NOTE: 📝

The relative entropy is currently computed by brute force, i.e., by enumerating all possible labelings of the leaves of the tree. This approach won't be feasible with large trees. so like, don't bring a giant tree to this party unless you want pain 😭

💖 sign-off 💖 This manual page is consEntropy 1.4, dated May 2016, and it's from the CONSENTROPY(1) manual. bye bestie, go slay your phylogenetics 🎀✨

📦 where this page comes from