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ssolo / ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
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geneFamily.treelist format #21

Closed ucassee closed 10 months ago

ucassee commented 3 years ago

Hi,

I want to follow your pipeline, but I don't know how to prepare the input files. Could you please provide a demo of geneFamily.treelist for me?

Thanks

Gullumluvl commented 2 years ago

Hi, it works with a file containing a list of Newick trees.

ssolo commented 10 months ago

Yes, thanks.