Rate variation and MAT updates#50
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- EM is now used for rate-variation (scalar) model. - User can specify maximum number of iterations for EM rate estimation for both rate-variation and site-specific-matrix models. Use "--rv-max-EM-steps <int>". - Added option to perform rate estimation after each tree traversal during SPR search. Use "--estimate-rates-during-SPR".
Updates to scalar rate variation model: - Estimate rates using nodes of type 0. - Take into account distance from last observation when estimating waiting times - Add pseudocounts - Use std min and max - Tidy code and reduce duplicate code
Fix bug in scalar rate variation estimation.
When writing out MATs, mutation support is now spread across all branches on the path between the nodes with the observations. When this path goes across the root, we consider separately the subpaths from the root and use the root distribution to estimate support.
Add details on rate-variation related options to usage_cmaple().
Add --estimate-MAT to usage_cmaple().
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