KH test on GARD results

[Oliveira-Hugo]

Dear @spond, I would like to know about the input for the KH test on GARD results from the current HyPhy implementation.

I note that after executing GARD I got the files:

• file.GARD.json
• file.best-gard
• file.best-gard.fit.bf

But none contains the trees for each partitions, which the KH test demands. I would like to know how to get the necessary inputs for the KH test.

Thank you so much for the attention.

combined_align.fasta.GARD.json combined_align.fasta.best-gard.fit.txt combined_align.fasta.best-gard.txt

[spond]

Dear @Oliveira-Hugo,

There is an old file in the HyPhy distribution hyphy kh, which will do crude KH tests on two trees. You can also do these types of tests on using IQTree (http://www.iqtree.org/doc/Advanced-Tutorial) or raxml.

You need to extract GARD partitions from the combined_align.fasta.best-gard file, and then test the alternative trees on them. hyphy no longer automatically does this.

In your particular example, all trees have 3 taxa, i.e., the same topology, so you can't run KH/SH tests on them (those tests assume different topologies).

Best, Sergei