The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
The Phylogenetic Tree server creates a distance or parsimony tree from a set of input sequences. It includes functionality for drawing the tree in several forms (radial, unrooted, rooted, phylogram or cladogram) with various other options.
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package.
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms
The TreeGen server takes as input a user-generated distance matrix and creates from it a distance-based phylogenetic tree.