Currently, only two different group maps are available for nucleotides: D1 and CYS. D1 contains conserved ring types only. In contrast to the groupmap D1, the colomap D1 contains all ambiguous nucleotides and. An additional colormap DC1 for the groupmap CYS exists as well. The naming is slightly inconsistent and confused me slightly.
I'd like to see all the different ambiguity codes in the consensus sequence as well, not only differently colored in the html output. Hence, I used -groupfile. But I recommend to make naming and content of color and group maps consistent.
Currently, only two different group maps are available for nucleotides:
D1andCYS.D1contains conserved ring types only. In contrast to the groupmapD1, the colomapD1contains all ambiguous nucleotides and. An additional colormapDC1for the groupmapCYSexists as well. The naming is slightly inconsistent and confused me slightly.I'd like to see all the different ambiguity codes in the consensus sequence as well, not only differently colored in the html output. Hence, I used
-groupfile. But I recommend to make naming and content of color and group maps consistent.