Optimal number of lambda values

[Nancy Dong]

Hello!

I am trying to do CAFE analysis on a large phylogenetic tree that contains both vertebrate and invertebrate species (12 species in total). 

I have tried to assign a different lambda value to each branch of the tree (26 lambda values in total), but that calculation was taking a very long time and I wasn't sure if it would finish. But I worry that if I use fewer lambda values, this would result in inaccurate results. So I would like to know if there is a rule of thumb or analysis for deciding on how many lambda values to use for a given tree?

Thank you very much!

Nancy

[Hahn, Matthew]

Hi Nancy,

If your tree has both vertebrates and invertebrates, it is almost certainly too deep to be analyzed by CAFE.  

But otherwise, starting with one lambda value is usually best, and in our experience the results are not so inaccurate under these conditions.  Searching for more lambdas should usually only be done if there is an explicit hypothesis about rate variation.

cheers,

Matt

--
You received this message because you are subscribed to the Google Groups "hahnlab-cafe" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hahnlabcafe...@googlegroups.com.
To post to this group, send email to hahnl...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hahnlabcafe/e7301fce-26bb-4abf-86c1-d26d2a56b038%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Matthew Hahn
Professor
Department of Biology & 
Department of Computer Science
1001 E. 3rd St.
Indiana University
Bloomington, IN 47405
Phone: (812)856-7001
http://www.indiana.edu/~hahnlab

[Nancy Dong]

Hello Matt,

Thank you very much for your quick reply! I will try CAFE analysis with only invertebrates and one lambda value then.

Best, 

Nancy