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.
Hello, I tried to reconcile a species tree and a gene tree, and I noticed that in the file with extension 'uml_rec', there are 100 proposed reconciled gene tree. I am wondering, does aleml search for the reconciliation that has the lowest likelihood, and all the gene trees in the uml_rec file have the same likelihood; or does aleml perform Monte Carlo simulation, and how is it different from alemcmc? and what is the temperature? Thanks.
Hello, I tried to reconcile a species tree and a gene tree, and I noticed that in the file with extension 'uml_rec', there are 100 proposed reconciled gene tree. I am wondering, does aleml search for the reconciliation that has the lowest likelihood, and all the gene trees in the uml_rec file have the same likelihood; or does aleml perform Monte Carlo simulation, and how is it different from alemcmc? and what is the temperature? Thanks.