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.TH GAINLOSS.SH "1" "November 2015" "gainLoss.sh 3.1" "User Commands"
.SH NAME
gainLoss \- Analysis of Phyletic Patterns in a Likelihood Framework
.SH 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
.SH USAGE
use a parameter file with these options:
.PP
_seqFile
.PP
_treeFile
.IP
_rootAt
_logFile
_logValue
_referenceSeq
_outDir
_outFile
_treeOutFile
_numberOfGainCategories
_numberOfLossCategories
_numberOfRateCategories
_maxNumOfIterationsModel
_epsilonOptimizationModel
_maxNumOfIterationsBBL
_epsilonOptimizationBBL
_epsilonOptimization
.IP
_gainLossDist
_calculateRate4site
_calculeGainLoss4site
_printTree
_printPij_t
_printLofPos
_performOptimizations
_isHGT_normal_Pij
_isReversible
\&...(a very partial list)
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