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Uploading tree block in nexus format (Read 5508 times)
smurray
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Uploading tree block in nexus format
Apr 22nd, 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  Smiley
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Sergei
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Re: Uploading tree block in nexus format
Reply #1 - Apr 22nd, 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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smurray
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Re: Uploading tree block in nexus format
Reply #2 - Apr 23rd, 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
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Re: Uploading tree block in nexus format
Reply #3 - Apr 23rd, 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 23rd, 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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Re: Uploading tree block in nexus format
Reply #5 - Apr 24th, 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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Re: Uploading tree block in nexus format
Reply #6 - Apr 24th, 2009 at 2:11pm
 
Thanks very much!   Grin
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