No MST

[Hollie Hatherell]

Hi I've got a fasta file of SNP data and I loaded this into phyloviz and ran goeBURST full MST. It runs but then nothing appears in the side panel, and it's not there when I double click on the dataset.

Thanks

Hollie

[Bitbucket user]

Hi,

Can you provide us some more information or, even better, a sample file so that we can try to reproduce the problem?

Thanks,

Alexandre

[Hollie Hatherell]

I have 403 samples with 261 variable sites, and some positions have 'N's. The sequences are quite similar, with the largest distance between any two pairs being 22 variants apart, and there is a proportion of samples that are identical (which I think was accounted for when I imported them - I got the message 'some profiles may have been discarded' when I imported the data)

Thanks, Hollie

[Bitbucket user]

Can you send us the output in Log Window? You can access it through View->Log.

Thanks, Alexandre

[Hollie Hatherell]

Log output

[Hollie Hatherell]

Output from running goeBURST Full MST

[Bitbucket user]

Sorry, I was asking for the PHYLOViZ log, the one that contains information about java version, software errors, etc. You should be able to access it though the top menu by clicking in View->log.

Thanks, Alexandre

[Bitbucket user]

Please, ignore my comment, you made it available already.

Thanks, Alexandre

[Bitbucket user]

I did some tests with several data sets including repeated sequences and I am not able to reproduce the problem. I notice that you are using the version 1.1. Can you try the version 1.1a available in download section? You should uninstall the previous version before. To run version 1.1a you can just unzip the file and run the right executable in directory bin for your OS.

[Bitbucket user]

Unable to reproduce.