TreeMerge is a tool for scaling phylogengy estimation methods to large datasets. TreeMerge can be used in a divide-and-conquer framework as follows: 1) divide the species set into disjoint subsets, 2) construct trees on each subset, and 3) combine the subset trees using an associated distance matrix (on the full species set). TreeMerge has been sucessfully tested in the context of species tree estimation (Molloy and Warnow, 2019).
If subsets are created by deleting edges from a starting tree, then the starting tree can be used to define the spanning tree on subsets given to TreeMerge as input. TreeMerge no longer uses the method described in Section 3.3 for deriving the spanning tree on subsets from a starting tree; it now uses the approach described in Theorem 9, but modified to handle the special case where edges that are less than two edges apart in the starting tree are deleted.
@article{MolloyWarnow2019,
author={Erin Molloy and Tandy Warnow},
title={{TreeMerge: A new method for improving the scalability of species tree estimation methods}},
year={2019},
journal={Bioinformatics},
note={in press}
}
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