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.
44
stars
15
forks
source link
Questions about the interpretation of ALE results #42
Thank you for the great software you have developed, it is very helpful for our research, I am new to phylogenetic problems and have encountered some confusing issues, I sincerely hope that you can give me some suggestions
For the ALEml_undated results I used branchwise_number_of_events.py to count the number of duplicates, transfers, losses, and origins for each branch, and in the first row of the image below, the branch number is shown as 118 for this branch, what does it represent on the species tree? How can I understand the meaning of this number? How can I visualise the species tree using itol, and how can I map it to the branches of the species tree? My impression. The phylogenetic tree has a node id and a tip id, but I'm not sure it represents the tip id
Can you give me any help? Sincere thanks in advance!
Hello, ALE team.
Thank you for the great software you have developed, it is very helpful for our research, I am new to phylogenetic problems and have encountered some confusing issues, I sincerely hope that you can give me some suggestions
For the ALEml_undated results I used branchwise_number_of_events.py to count the number of duplicates, transfers, losses, and origins for each branch, and in the first row of the image below, the branch number is shown as 118 for this branch, what does it represent on the species tree? How can I understand the meaning of this number? How can I visualise the species tree using itol, and how can I map it to the branches of the species tree? My impression. The phylogenetic tree has a node id and a tip id, but I'm not sure it represents the tip id
Can you give me any help? Sincere thanks in advance!
Best, xnw