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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Removed Random.all, included RandomTools.h explicitly #5
The generic include files (*.all) were
removed from Bio++ Library in January 24, 2013
in commit d39443f.
Because of that Bio++ 2.10, 2.20 and
development versions don't have
the Random.all header file anymore.
This change should be backwards compatible as
Bpp/Numeric/Random/RandomTools.h wasn't
changed after the Random.all header file
was introduced in Bio++ commit 8b39bc0 in
December 10, 2010.
The generic include files (*.all) were removed from Bio++ Library in January 24, 2013 in commit d39443f.
Because of that Bio++ 2.10, 2.20 and development versions don't have the Random.all header file anymore.
This change should be backwards compatible as Bpp/Numeric/Random/RandomTools.h wasn't changed after the Random.all header file was introduced in Bio++ commit 8b39bc0 in December 10, 2010.
https://github.com/BioPP/bpp-core/commit/d39443f https://github.com/BioPP/bpp-core/commit/8b39bc0