Reconstruction of ancestral gene content

[wenhao li]

Hello, I want to use the genome and one of the gene families of some bacteria to judge whether this gene of their common ancestor exists.
When I run alarax-fdata/test/families.txt-sdata/test/itol.treefile-p output _ test _ recombination-gene-tree-samples 100.

There are 100 files of family0-family99 in the output _ test _ reconciliation \ reconciliation \ all directory. Which one should I use to judge the reconciliation result?

[wenhao li]

In addition, how to get PP value?

[Benoit Morel]

Hello,

Each of the 100 reconciliation files is one sample drawn randomly from the reconciliation distribution. I you want to judge whether the gene is present in the common ancestor, you can count how frequently this happens in the 100 samples,

Benoit

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