[EMBOSS] consensus sequence from Prettyplot and Cons

[Peter Rice]

forward at hongyu.org wrote:
> Hi there,
> 
> I am new to this group, sorry if it's a discussed question here.
> 
> I found there is difference between the consensus sequences generated for
> the same alignment by the two programs: Prettyplot and Cons. I've tried
> adjusting the parameters such as -plurality and -identity, but failed to
> reconcile the two no matter how.
> 
> Please let me know if you have met the same problem or whether you have
> good solution to it. Thanks!

We do have multiple copies of the consensus calculation in the current EMBOSS 
code. There are also different options for calculating the consensus which can 
affect the results you see. The -plurality and -identity should change only 
how the individual sequences are shown, I do not expect them to change the 
consensus sequence (but I may be wrong!).

Can you send me:

the aligned sequence input

the command line for prettyplot

the command line for cons

regards,

Peter Rice