Remove amap_msa, add t_coffee_pair, 3dcoffee_msa, mafft_msa
Remove amap_msa, add t_coffee_pair, 3dcoffee_msa, mafft_msa

AMAP has been discontinued by its authors.

Also reorder methods as in t_coffee help.

anilthanki/tgac-galaxytools,TGAC/earlham-galaxytools,TGAC/earlham-galaxytools,TGAC/earlham-galaxytools,anilthanki/tgac-galaxytools,anilthanki/tgac-galaxytools,TGAC/earlham-galaxytools,TGAC/earlham-galaxytools,anilthanki/tgac-galaxytools,anilthanki/tgac-galaxytools