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Uploading tree block in nexus format (Read 5510 times)

smurray

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Uploading tree block in nexus format
Apr 22^nd, 2009 at 6:39pm

Hi Sergei,

I am wondering if you can help with something. I am doing GAbranch analyses in datamonkey. I would like to specify a tree rather than use the default NJ tree, as I have done ML analyses with a much broader group of sequences and I trust that topology.

When I upload the data file in nexus format, for some reason it doesn't seem to read the trees block. No tree comes up in the window. I am not sure what to try?

many thanks

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Sergei

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Re: Uploading tree block in nexus format
Reply #1 - Apr 22^nd, 2009 at 8:38pm

Dear smurray,

If you open the same alignment in HyPhy, is the tree read properly? You can check by seeing if there is a tree in the Object Inspector (from the 'Windows' menu).

Most commonly the tree will be discarded by Datamonkey if leaf names and taxon names are not matched. I can take a look if you paste in your datamonkey job ID (upload.numbers.1).

Cheers,
Sergei

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Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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smurray YaBB Newbies Offline Feed your monkey! Posts: 13	Re: Uploading tree block in nexus format Reply #2 - Apr 23^rd, 2009 at 5:25am Hi there, I tested it in HyPhy, and the tree did not come up in the object inspector window there either. It seems that the taxon names are identical...which I would expect since I made the tree from that data file. The job upload ID is Job ID:upload.65367939356782.1 Many thanks
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Uploading tree block in nexus format Reply #3 - Apr 23^rd, 2009 at 8:50am Dear smurray, In the NEXUS file that you uploaded, the `data` block was not terminated using the `end;` statement. If you add `end;` right before the `begin trees;` statement, HyPhy (and datamonkey) will recognize the tree. Cheers, Sergei
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smurray

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Re: Uploading tree block in nexus format
Reply #4 - Apr 23^rd, 2009 at 10:53pm

Dear Sergei,

I did try changing the nexus format in case that was the problem, as I wasn't certain whether it needed the end; statement or not.

I previously uploaded a file that did have the end; before the begin trees block
Job ID:upload.688386314817855.1

It also didn't recognise the trees block and nothing came up with Hyphy.

Not sure what to try now? Can you upload a tree in a phylip format file?

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Uploading tree block in nexus format Reply #5 - Apr 24^th, 2009 at 7:46am Hmm, Not sure what's going in. I will look into it. In the meantime, if you move the tree block BEFORE the data block, it will be recognized. Sergei
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smurray YaBB Newbies Offline Feed your monkey! Posts: 13	Re: Uploading tree block in nexus format Reply #6 - Apr 24^th, 2009 at 2:11pm Thanks very much!
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