SATé

Description: Simultaneous Alignment and Tree Estimation (SATé) is a software package for constructing phylogenies and alignments from sequence data.

Publications: Liu et al. (2009), Liu et al. (2011)

Download: Download SATé

PhyloNet

Description: A suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa.

Publications: Than et al. (2010)

Download: Download PhyloNet