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  :)

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

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

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

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?

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

Thanks very much!   ;D