Error importing nexus files to Beauti

[Karen Poole]

Hi all,

When I try to import my data into Beauti, I get the following error message: "Error parsing imported file: dr.evolution.io.Importer$ImportException: Expecting ';' after sequences data, has '?' in line 57."

Line 57 is the last line of my data matrix, so it has quite a few question marks.  I've tried moving the semi-colon at the end of the data matrix around just to see if I can import the file, with no results.  I have no trouble importing the example files, and I can open the file with my data in other programs.  Any ideas as to what the problem might be?

In case this info is helpful, my data was compiled in Mesquite.  I exported the nexus file from there, both in MrBayes and simplified nexus formats.  Neither one worked.

Thanks,

Karen

[Natalia]

Hello Karen,

I am by no means an expert in this, but I had similar errors and there were caused by the taxon names not being identical in all of my partitions. It seems though that you just have one partition. Also, Mesquite adds sometimes elements that are not recognized from other programs such as the symbols command before the character matrix. If you want, you can send your nexus file and I will have a look. 

Natalia

[Karen Poole]

Thanks Natalia,

You're right that I only have one partition at the moment, so that shouldn't be the issue.  I'm attaching the nexus file here--if you can see what's wrong with it I'd really appreciate it!

Karen

[Natalia Chousou-Polydouri]

Hello Karen,

I think I found the problem. I think it is the way you code polymorphisms {0 1}. I replaced a character on a binary matrix of mine with the above notation and I got pretty much an identical error. Without the polymorphism, the file is imported fine in beauti.

Unfortunately, I don't know how beast can read polymorphic states. Maybe there is a different notation for polymorphism for the standard datatype? Or you should define a new state for the polymorphism (like the ambiguity codes in DNA) and replace this notation in your file. Then in order for the ambiguities/polymorphism to be taken into account and not be treated as missing data, you should check the use ambiguities box.

sorry for not being able to help more,

Natalia

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[Karen Poole]

Yes--that's the problem!  I tested it by replacing the polymorphisms with question marks, and was able to import the file.  I'll look into different ways of coding those states (likely using separate states to represents polymorphisms).

Thanks so much for your help!

Karen

[Manabu Sakamoto]

Hello,

Did this issue get resolved? I'm having exactly the same problem; I can't import NEXUS file into BEAUTi because of multi-state characters.

many thanks,

Manabu

[Manabu Sakamoto]

Just as a follow up in case anyone wanted an answer to this issue, I figured out that multistate characters need to be in curly braces "{ }" instead of parentheses "( )" in order for NEXUS files to be read into BEAUti. 

[Nicole Veto]

Hi everyone,

I had the same problem. But, how I didn't the have these characters between {} or [], Manabu warned about the spaces in the taxons name. Now everything is working normally.

Cheers,

Nicole