/usr/local/phylogeny/phyml/bin/phyml -i input_files/20110223_224120/input.txt -d codon -b 0 -f e --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11" -c 1 --mechanistic_opt 01000 -o lr --mechanistic_params "-9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0"


. Sum=1.000003
. Scaling frequencies...

. The number of taxa cannot be negative.