Help with Beauti input file

[Nicolette Van Zyl]

Dear Beast users

I have a dataset that contains sequences of different lengths.I do not want to trim these to be the same length as all the samples are full coding region.  Is there any way to incorporate these sequences into a nexus file so that beauti will accept this?

I get the following error: error parsing imported file: dr.evolution.io.importer$importexception.

Can anyone help?

Regards

Nicolette

[Gerald Schneeweiss]

Dear Nicolette,

add N's at the end(s) of the sequences as necessary to get sequences of
equal length.

Best,
Gerald

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[Andrew Rambaut]

Hi Nicolette,

Are these sequences aligned? An alignment program should pad the extra spaces with gaps.

Andrew

[Nicolette Van Zyl]

Hi

Yes these sequences are aligned, however when aligning in clustal the program adds so many gaps that the sequences are in fact not really aligned.  this is a very variable gene and it seems to create some problems.

I tried the suggestion of adding some N's at end but I still get the error when loading in Beauti.

Do you perhaps have some other suggestion?

regards

Nicolette