Clustal Omega is a multiple sequence alignment program. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries).