Fixing Newick Starting Tree in SNAPP

Paul Maier

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Jun 7, 2019, 5:24:08 PM6/7/19

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Hi,

When trying to substitute the UPGMA starting tree in SNAPP with a specified Newick tree, I run into an error.

The line I substitute is this one:

In exchange for this one:

I have read this article about BEAST starting trees, as well as several related Google Groups forums, but none of the suggested fixes has so far worked:

https://www.beast2.org/2014/07/28/all-about-starting-trees

The error is this familiar line:

validate and intialize error: Label 'God_K101' in Newick beast.tree could not be identified. Perhaps taxa or taxonset is not specified?

Where the labels (e.g. God_K101) in the Newick tree are identical to the labels in the alignment.

Little help?

Remco Bouckaert

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Jun 9, 2019, 7:29:53 PM6/9/19

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Hi Paul,

Are you perhaps mixing taxa for the sequences with those of the species tree? Note that if taxa names for the species equal that of the gene, BEAUti automatically can add a number to the species id to guarantee they are uniquely named. So, if ‘God_K101’ is the id for a sequence, possibly the species taxon can be ‘God_K1011'.

Cheers,

Remco

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Paul Maier

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Jun 11, 2019, 11:59:29 PM6/11/19

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Hi Remco,

Yes, you were exactly right. I was specifying a tree containing all taxa, not the species tree. That fixed my problem.

Thanks!

Paul

On Sunday, June 9, 2019 at 6:29:53 PM UTC-5, Remco Bouckaert wrote:

Hi Paul,

Are you perhaps mixing taxa for the sequences with those of the species tree? Note that if taxa names for the species equal that of the gene, BEAUti automatically can add a number to the species id to guarantee they are uniquely named. So, if ‘God_K101’ is the id for a sequence, possibly the species taxon can be ‘God_K1011'.

Cheers,

Remco

On 8/06/2019, at 8:21 AM, Paul Maier <mai...@gmail.com> wrote:

Hi,

When trying to substitute the UPGMA starting tree in SNAPP with a specified Newick tree, I run into an error.

The line I substitute is this one:
<stateNode id="tree" spec="beast.util.ClusterTree" clusterType="upgma" nodetype="snap.NodeData">

In exchange for this one:
<stateNode id="tree" spec="beast.util.TreeParser" IsLabelledNewick="true" nodetype="snap.NodeData" newick="(Taxon_A(Taxon_B,Taxon_C));">

I have read this article about BEAST starting trees, as well as several related Google Groups forums, but none of the suggested fixes has so far worked:
https://www.beast2.org/2014/07/28/all-about-starting-trees

The error is this familiar line:
validate and intialize error: Label 'God_K101' in Newick beast.tree could not be identified. Perhaps taxa or taxonset is not specified?

Where the labels (e.g. God_K101) in the Newick tree are identical to the labels in the alignment.

Little help?

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