IQ-TREE: Phylogenomic inference by maximum likelihood
Efficient tree reconstruction for phylogenomic data, ultrafast approximation for phylogenetic bootstrap, ultrafast model selection. IQ-TREE supports a wide range of evolutionary models and high performance computing.
MPBoot: Maximum Parsimony Bootstrap
An efficient software to reconstruct phylogenetic trees by maximum parsimony and ultrafast bootstrap.
DecentTree: Scalable Neighbour-Joining for the genomic era
Highly optimized and parallel implementations of Neighbour-Joining and several of its variants.
CMAPLE: Efficient phylogenetic inference in the pandemic era
A highly optimized phylogenetic inference package designed for pathogen data, which includes standalone software and a C++ library.