GAINLOSS.SH(1)

📦 version 3.11, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ NAME ✨

gainLoss — Analysis of Phyletic Patterns in a Likelihood Framework 💅

okay bestie, this is the GAINLOSS.SH(1) manual page from the User Commands section, and the command is literally gainLoss. no cap. 🫶

💖 DESCRIPTION 💖

The gainLoss project: Analysis of Phyletic Patterns in a Likelihood Framework ✨

Version: gainLoss.VR01.266 - last updated 14.10.2013 📅

Ofir Cohen - ofircohe@tau.ac.il 💌

🦋 USAGE 🦋

okay so the usage is literally: use a parameter file with these options, bestie. it's giving config-file main character energy. 👑

  • _seqFile
  • _treeFile
  • _rootAt
  • _logFile
  • _logValue
  • _referenceSeq
  • _outDir
  • _outFile
  • _treeOutFile
  • _numberOfGainCategories
  • _numberOfLossCategories
  • _numberOfRateCategories
  • _maxNumOfIterationsModel
  • _epsilonOptimizationModel
  • _maxNumOfIterationsBBL
  • _epsilonOptimizationBBL
  • _epsilonOptimization
  • _gainLossDist
  • _calculateRate4site
  • _calculeGainLoss4site
  • _printTree
  • _printPij_t
  • _printLofPos
  • _performOptimizations
  • _isHGT_normal_Pij
  • _isReversible

and yes, the page itself says ...(a very partial list) — so that's literally not all of them, bestie. 😭

💖 mwah, that's the whole thing! this page is from gainLoss.sh 3.1, dated November 2015. periodt. 💅✨

📦 where this page comes from