jModeltest 2.1.10 command : -tr 56 -d alignment.phy -s 3 -i -g 8 -f -AIC -o jmodeltest.out
Best model : HKY+I+G
Phyml 20130103 command : phyml -i alignment.phy -d nt -n 1 -b 0 --run_id HKY+I+G -m 010010 -f m -v e -c 8 -a e --no_memory_check -o tlr -s BEST
The phylogeny is done with the non-redundant sequences when possible because a structure similarity is needed.