---
name: "gainLoss"
section: "1"
platform: "linux"
package: "fastml"
version: "3.11-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gainLoss"
---

# gainLoss(1)

Analysis of Phyletic Patterns in a Likelihood Framework

## NAME

gainLoss - Analysis of Phyletic Patterns in a Likelihood Framework

## 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

use a parameter file with these options:

\_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 ...(a very partial list)