Using indels as bipartition in BEAST2 (with STACEY)

[Naka Kaburagi]

Dear all,

I am trying to run a multilocus analysis using STACEY in BEAST2. I have dna alignments for 30 loci, and I would like to add more information into the analysis by using the indels. I coded them into seperate binary files. I loaded the dna alignments and indels binary alignments (making a total of 60 files). I used to do it on BEAST using *BEAST, I have found a post in this group explaining how to make it work by changing "id=frequencies" and "id=siteModel" for the indel partitions. But I don't know how to make it work on BEAST2 with STACEY. I get the error: "Fatal exception: 10". This does not help me to understand where is the problem...

Can anyone help me?

Thanks

Stella

[Naka Kaburagi]

Dear all,

I am trying to run a multilocus analysis using STACEY in BEAST2. I have dna alignments for 33 loci, and I would like to add more information into the analysis by using the indels. I coded them into seperate binary files. I loaded the dna alignments and indels binary alignments (making a total of 66 files). I used to do it on BEAST using *BEAST, I have found a post in this group explaining how to make it work by changing "id=frequencies" and "id=siteModel" for the indel partitions. But I don't know how to make it work on BEAST2 with STACEY. I get the error: "Fatal exception: 10". This does not help me to understand where is the problem...

[Graham]

Naka,

It looks like the error is in the substitution model (....JukesCantor.getTransitionProbabilities). I don't know how to set up indels in BEAST2. I hope someone else can help with that.

Graham