BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.

ABSTRACT: Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recently, we introduced Bad Clade Deletion (BCD) supertrees which combines the graph-based computation of minimum cuts with optimizing a global objective function on the matrix representation of the input trees. The BCD supertree method has guaranteed polynomial running time and is very swift in practice. The quality of reconstructed supertrees was superior to matrix representation with parsimony (MRP) and usually on par with SuperFine for simulated data; but particularly for biolo

SUBMITTER: Fleischauer M 

PROVIDER: S-EPMC5995099 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature