/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_164930/input.phy -d codon -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 0.0 0.0001 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace


. Sum=1.000003
. Scaling frequencies...

. The scale_param_b for rate variation over sites has been specified; unreasonable values tend to be estimated for scale and w_0.

. Err: bad symbol: "M" at position 86 of species African_elephant.NC_000934