Malign [more
information]
The multiple alignment procedures implemented
in MALIGN are close parallels to those used to search for
minimum length cladograms. The logic and program commands
will be clear to those familiar with programs such as Hennig86,
NONA, and PAUP. Alignment topologies are constructed via
different sequences and improved through branch swapping.
Each alignment topology yields a multiple alignment and
cladograms are constructed from that alignment. The cost
of the most parsimonious cladogram is then assigned as the
multiple alignment cost.
POY [more
information]
POY is a program for phylogenetic analysis that allows the homology of genomic (nucleotides, genes and gene regions, chromosomes, whole genomes) and other data (e.g., morphology, behavior) to be evaluated dynamically by optimizing them directly onto topologies using either parsimony or maximum likelihood optimality criteria. This dynamic homology assessment leads to solutions that are generally less costly than can be attained through multiple sequence alignment followed by tree searching. A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.
In addition to numerous heuristic dynamic homology algorithms, POY implements heuristic tree search strategies like branch swapping, simulated annealing, tree fusing, and ratcheting, making it an efficient tool for analyzing static matrices as well. It also permits evaluation of support (Bremer support, resampling measures) and visualization of results.
With the release of POY4 we have created a POY4 mail group for users to post questions and bugs and find information on using POY.
