Hello,

I am estimating the rates for several alignments from the same species simultaneously, but would like to fix the branch lengths between them.  Is there any way to set branch length as a global variable?

Also, is there any way to get around HYPHY being unable to estimate negative numbers?

Thanks,

Mike

Hi Mike,

Yes, you can fix the branch length -- take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

My apologies in advance, HyPhy exposes a lot of the underlying machinery and makes branch length constraints somewhat obtuse.

You can allow negative values for a parameter in HyPhy batch files to remove the (implicitly enforced) 0 lower bound by including the line(s):

[code]

paramaterName :> -1e-25;

[/code]

to reset the lower bound to some (large) negative value.

Sergei