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.
When I run ALE, I got some problems. When I sought to reconstruct gene family histories with amalgamated likelihood estimation (ALE), I encountered some difficulties. I found a speciation event of a gene family in a node. I couldn't find any speciation event before this node, and instead, I got a HGT event. It confused me that a speciation event happened after a HGT event. May I need to change the parameter or it is the true case that you have met. Could u pls help me solve this problem? I'd be grateful if you could help me. Thank you.
When I run ALE, I got some problems. When I sought to reconstruct gene family histories with amalgamated likelihood estimation (ALE), I encountered some difficulties. I found a speciation event of a gene family in a node. I couldn't find any speciation event before this node, and instead, I got a HGT event. It confused me that a speciation event happened after a HGT event. May I need to change the parameter or it is the true case that you have met. Could u pls help me solve this problem? I'd be grateful if you could help me. Thank you.