XML imported tree problem

[Alexandra Herrera]

I'm trying to include an ML tree for a *Beast analysis, and I'm getting this error:

Error parsing '<newick>' element with id, 'null': 

error parsing tree in newick element - Missing closing ')' in tree

I've open the same tree file in mesquite and figtree with success. I checked the xml file for spaces in the newick tree, but there are none. I even checked the tree file for the number of parentheses, there are the same number of open and close parentheses. I had imported ML trees for other two datasets without problem.

Does anyone have any suggestions? thanks in advance,

Alexandra

[Alexei Drummond]

Is your tree rooted with a bifurcation at the root? Most ML programs don’t estimate a rooted tree, so they will typically have an arbitrary rooting with a trifurcation at the root. That sort of tree is an illegal starting tree in BEAST. BEAST only considers binary trees.

Alexei

--
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 http://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

[Alexandra Herrera]

Hi Alexei,

yes my tree is completely bifurcate, it is a RaxML tree. Could you look at my tree, the xml file from Beauti, and the Beast run? thanks again,

Alexandra

[Alexandra Herrera]

I'm having the same problem Missing closing ')' in tree with other data sets. I'm using Beast v 1.8.2. Does anyone have a suggestion? 

Alexandra

[Graham]

Your tree is not ultrametric, which it must be for BEAST. I don't know why you get that error message.

[Alexandra Herrera]

Thanks Graham for the suggestion. I changed the tree to ultrametric, now I got this problem:

Error parsing '<newick>' element with id, 'null':

error parsing tree in newick element - Expecting ',' in tree, but got ' '

my tree is bifurcated, any more suggestions?

Alexandra

[Graham]

Do you have your computer set up so that the decimal point is represented as a comma? (I think that might confuse BEAST.)

[Alexandra Herrera]

 Thanks for the tip but no, my computer displays decimals as points. Another idea on how to solve this problem?

--
You received this message because you are subscribed to a topic in the Google Groups "beast-users" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/beast-users/rf4h86OVshY/unsubscribe.
To unsubscribe from this group and all its topics, send an email to beast-users...@googlegroups.com.

[Nick Matzke]

Read the tree into FigTree, double check that the root is fully resolved, and/or re-root it to be sure, then save that out to Newick as it's displayed, then paste that Newick in (?).

Cheers, Nick

[Alexandra Herrera]

I finally go my xml file running. I change two things in the newick tree on the xml file:

1. change the branch lengths from scientific for decimal notation, and

2. put the newick tree in just one line, Beauti was cutting it in 3 lines

I hope this helps someone else with the same problem,

Alexandra

[Ashok Mallik]

Hi Alexandra, 

I am running through same problem! Can you please suggest me how can I convert RAxML tree to use in BEAST?

Thanks

Ashok