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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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Docker version works on Windows, Compiled version throws NodePException error on Linux #17

Closed Biogeographer closed 1 year ago

Biogeographer commented 5 years ago

The attached gene tree (G.tree) runs successfully in ALEobserve on both Windows and Linux systems yielding the expected output comprising marginal clade frequencies (G.trees.ale; attached from Windows). However, ALEmcmc_undated completes and exists normally on Windows but terminates with the error below on Linux.

terminate called after throwing an instance of 'bpp::NodePException' what(): NodeException: Node::getDistanceToFather: Node has no distance.(id:0)

I assume this is an issue with the trees in my examples having no branch lengths. However, why does Windows allow trees without branch lengths for the undated algorithm, and Linux does not?

I am running ALE v. 0.4 on Windows 10 Pro pulled from Docker and ALE v. 0.5 on a Linux Server running Centos 6.6.

Thank you kindly!

ale-example.zip

neptuneyt commented 2 years ago

I have the same problem, do you have any solution? Thanks a lot.

ssolo commented 1 year ago

Sorry, don't know docker, maybe @Boussau can help!