no block of taxa could be created from a MrBayes .con tree

The upoad of the attached file fails: it says it cannot generate a block of taxa. This is either a bug or a strong limitation: the file contains a nexus tree obtained from MrBayes; it should not be so special.

Reported by: blaiseli

Original comment by: blaiseli

Thanks for reporting this bug. We'll look into it as soon as possible.

Original comment by: piel

This looks like a difficult bug to fix because the problem stems from Mesquite. I'm puzzled why Mesquite cannot create a default taxon block from a tree block that does not use a translation table. I've tried opening trees like this in Mesquite v. 2 with no success...

Original comment by: piel

• priority: 5 --> 8

Original comment by: piel

The issue is because, although mesquite can create a taxa block on the fly while reading a tree block without a translation table, it doesn't want to. It prods the user for feedback, which makes the import hang in headless mode. Bill has emailed the Maddisons about this, and it looks like the issue could certainly be fixed in their code (even if that would make it some sort of treebase special). But - then we have to fold that change into our previous treebase special version of mesquite, which was a snapshot roughly at version 2.1, and we're now at 2.6. I did some testing and some methods have changed or have been removed, so we would need to adapt our code base to that new api.

Original comment by: rvosa

This has been downgraded. We can't fix this unless mesquite gets fixed. If people want to upload mrbayes files they will have to run them through mesquite first on their own machines.

Original comment by: rvosa

• priority: 8 --> 7
• assigned_to: mjdominus --> rvos

Original comment by: rvosa

I think this needs to be closed: there is simply no way we will ever support all nexus variants. It is a feature of treebase that we support mesquite-compatible files. We state this very clearly. If people decide to upload files that are not compatible with mesquite there's not much we can do.

Original comment by: rvosa

We won't fix this directly because we can't support all variants of NEXUS. However, we should better document which NEXUS versions we do support, and at some point we may also switch out Mesquite as the NEXUS parser to another one, e.g., NCL. (Though no NEXUS parser can be expected to support all flavors.)

Original comment by: hlapp

• priority: 7 --> 2

Original comment by: hlapp

Thanks for reporting this bug. We'll look into it as soon as possible.

Original comment by: rvosa

OK, I am assigning this to "None". It is pointless to pretend that this is a fixable bug. To be able to read MrBayes trees we will have to switch to a newer mesquite. This is not a task that is properly assigned to me. I will not do this.

Original comment by: rvosa

• assigned_to: rvos --> nobody

Original comment by: rvosa