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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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ALE installation #4

Closed ag8525 closed 7 years ago

ag8525 commented 7 years ago

Hello,

I am trying to install and use ALE on computer cluster. Is there any detailed and easy manual to install and run the program?

Specifically, the make command is looking for Bpp/Numeric/Random.all file which does not exist in bpp libraries. Any suggestions?

I would really appreciate any help,

Thank you

ssolo commented 7 years ago

@ag8525 we are working on detailed and easy instructions.

Re, the issue you cite, to compile ALE you will need the Bio++ libraries, which you can install as described here: http://biopp.univ-montp2.fr/wiki/index.php/Installation

drenal commented 7 years ago

Dear ag8525,

Does your issue still persist?

We created a HowTo for openSUSE systems and it's a good starting point for other distributions too.

The Random.all-bug was resolved with commit d6f5a40.

Regards, Lenard

ssolo commented 7 years ago

I'm closing this no the assumption that it has been resolved. Please reopen if this is not the case.