table of contents
GAINLOSS.SH(1) | User Commands | GAINLOSS.SH(1) |
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)
November 2015 | gainLoss.sh 3.1 |