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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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Before, when no build type was specified, cmake's default compile flags were set (resulting in errors on newer compilers). Now, the compile flags specified in CMAKE_CXX_FLAGS_DISTRIBUTION are used.
6370cfeView on GitHubThe Bio++ libraries are now automatically downloaded, patched and linked against ALE, without the user needing to install them at all. Boost is downloaded and built, if not found on the system. Install.md has been updated to notify the user of not needing to download boost or Bio++.
112602bView on GitHubadded originate only on specifed branch option, i.e. 6.6th example: fixed multiplier for Origination on branch 43 to 1 and zero elsewhere (no origination outside 43)\n ./ALEml_undated species_tree.newick gene_tree_sample.ale rate_multiplier:O:43:-1
c5b08dfView on GitHubAdded fixed D/T ratio ML and use SimpleMultiDimensions optimizer instead of DownhillSimplexMethod for >3D.
3cab591View on GitHub