I’m not sure whether it is still proper to post this here: We created and are actively developing the IQ-TREE open-source software for phylogenomic inference at http://www.iqtree.org. IQ-TREE is especially suited to analyze NGS data and has perhaps the most comprehensive sets of maximum likelihood models available to date incl. common DNA, protein, codon models as well as complex partition, mixture, CAT, heterotachy models, etc. IQ-TREE offers fast tree search, model selection (ModelFinder), ultrafast bootstrapping (UFBoot) and many other features.
IQ-TREE has a good documentation (http://www.iqtree.org/doc/), user support (https://groups.google.com/d/forum/iqtree) and a free online web service (http://iqtree.cibiv.univie.ac.at/).
IQ-TREE is the successor of the IQPNNI and TREE-PUZZLE software.
Minh and the development team.