Evo rate calculations with eukaryotic whole-genome data

[seth redmond]

I'm trying to do some evolutionary rate calculations with heterochronous whole-genome sequences of a eukaryote. As it's obviously too large to present BEAST with a whole-chromosome alignment I'm encoding these as binary states in my nexus file, however as a result my rate calculations are hugely inflated. Is there any way I can set the invariant sites without adding many-megabases-worth of 0s?

Also, has anyone else managed to successfully perform this kind of study using genome-wide sequence of a eukaryote?

[Remco Bouckaert]

Hi Seth,

Perhaps, this is what you are looking for: https://groups.google.com/d/topic/beast-users/QfBHMOqImFE

Cheers,

Remco

On 10/12/2016, at 5:45 AM, seth redmond <seth.r...@gmail.com> wrote:

I'm trying to do some evolutionary rate calculations with heterochronous whole-genome sequences of a eukaryote. As it's obviously too large to present BEAST with a whole-chromosome alignment I'm encoding these as binary states in my nexus file, however as a result my rate calculations are hugely inflated. Is there any way I can set the invariant sites without adding many-megabases-worth of 0s?

Also, has anyone else managed to successfully perform this kind of study using genome-wide sequence of a eukaryote?

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at https://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

[seth redmond]

Ah, that's exactly what I'm after. Thanks!

-s