What does "speciation_or_duplication" mean?

Skip to first unread message

Anting Xu

Aug 21, 2013, 9:47:02 PM8/21/13
to archae...@googlegroups.com
Hi there,

I am a little confused by the event type "speciation_or_duplication" produced by the following code:

java -Xmx1000m -cp forester_1028.jar org.forester.application.gsdi -g gene.phyloxml species.phyloxml out.phyloxml

When I add the -m parameter to the above code, Forester converts all of them to speciation.

Does that mean forester is not sure about the event assignment? Also can any one direct me to a paper / document that talks about this ambiguous assignment?

Thanks a lot for your time.


Christian Zmasek

Sep 1, 2013, 5:37:59 AM9/1/13
to archae...@googlegroups.com, anti...@gmail.com
Hi Anting,

speciation_or_duplication is needed in cases where the species tree contains polytomies (nodes with more than two children). Because in such cases not all nodes in the gene tree can be assigned with certainty.

If the species tree is completely binary, speciation_or_duplication is never used.


> From: Anting Xu <anti...@gmail.com>
>To: archae...@googlegroups.com
>Sent: Wednesday, August 21, 2013 6:47 PM
>Subject: [Archaeopteryx] What does "speciation_or_duplication" mean?

>You received this message because you are subscribed to the Google
>Groups "Archaeopteryx" group.
>To unsubscribe from this group, send email to
>For more options, visit this group at
>You received this message because you are subscribed to the Google Groups "Archaeopteryx" group.
>To unsubscribe from this group and stop receiving emails from it, send an email to archaeoptery...@googlegroups.com.
>For more options, visit https://groups.google.com/groups/opt_out.

Reply all
Reply to author
0 new messages