mtree is a set of softwares for constructing Hyplogenetic Networks from Multiple Phylogenetic Trees.
CMPT (Programs for Computing MAAF, MAAFs, MAF, MAFs of Multiple Phylogenetic Trees) are Programs for computing a maximum agreement forest (MAF) , all maximum agreement forests (MAFs) , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two or more given phylogenetic trees. Once our programs find an MAAF, they also construct a reticulate network with the minimum number of reticulation vertices.
MaafB are programs for estimating lower bounds on the reticulation numbers of reticulate networks for multiple phylogenetic trees.
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IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2):372-84. doi: 10.1109/TCBB.2011.137
Algorithms for Reticulate Networks of Multiple Phylogenetic Trees.
Chen ZZ, Wang L.