# This file contains the list of meta parameters of comparative gene prediction which are subject to optimization. 
# All other meta parameters are chosen as given in the species parameter file. The order 
# of the parameters determines the order in the optimization process.
# Basically, different values for these meta parameters are tried out and the ones
# giving best performance on the evaluation set are chosen.
# For each parameter the range of possible values is specified after the parameter
# name and at least one white space.
# 3 cases are possible for the range:
# - an explicit list is given, e.g. protein	"on" "off"
# - it is an integer range, e.g. window_size	"1"-"5"
# - it is a range of floating point numbers, e.g. pseudocount	"0.3"_"1.8"
#
# 
# Stefanie Koenig, 29.7.2014
#

/MeaPrediction/x1_E	"5"_"500"
/MeaPrediction/x1_I	"10"_"1000"
/CompPred/phylo_factor	"1"-"5"
/CompPred/exon_gain	"0.01"_"0.000001"
/CompPred/exon_loss	"0.01"_"0.000001"
/CompPred/ec_addend	"-30"_"-10"
/CompPred/ec_factor	"1"_"6"
# comment parameters out that you do not want to be subject of optimization
#/MeaPrediction/i1_E
#/MeaPrediction/i1_I
#/MeaPrediction/i2_E
#/MeaPrediction/i2_I
#/MeaPrediction/r_be
#/MeaPrediction/r_bi
#/MeaPrediction/y0_E
#/MeaPrediction/y0_I
#/MeaPrediction/x0_E	
#/MeaPrediction/x0_I	
#/MeaPrediction/alpha_E
#/MeaPrediction/alpha_I
#/MeaPrediction/j1_E
#/MeaPrediction/j1_I
#/MeaPrediction/j2_E
#/MeaPrediction/j2_I
