Molecular phylogeny
Molecular phylogeny employs nucleotide sequences (or some character depending on sequences) from several organisms to compute the tree connecting the data and requiring fewest steps. "Steps" are the individual mutations (substitutions, insertions, etc.) required to transform the sequence of one species into that of another. One can create trees from nucleotide sequences, transversions (a subset of nucleotide sequences), amino acid sequences, indels (insertions and deletions), etc. Reliability of trees can be tested. One can, for example, create different trees (e.g. nucleotide sequences and indels, nuclear nucleotide sequences and mitochondrial nucleotide sequences). One can form trees from subsets of nucleotide sequences. If trees agree, the process is reliable. This, of course, requires appropriate data sets and procedures. For example, too small a data set can give an unreliable tree. Deep divergences require characters that change slowly since rapidly changing steps may be saturated (as when a trail of footprints is overwhelmed by other trails).
One finds (provided a large data set and appropriately resolved steps) these trees to be congruent with each other and largely congruent with accepted trees created from anatomy and the fossil record using cladistics. One finds a contiguous and connected tree without obvious breaks representing species or "kinds" or reflecting a break between micromutations and macromutations.
Molecular phylogeny provided new, powerful, and independent tests of the theory of evolution. Evolution required molecular phylogeny to be consistent with classical phylogeny. It also predicted that all parts of the genome should evolve in parallel and exhibit the same taxonomic pattern. In all respects molecular phylogeny amply confirmed the theory of evolution.
Molecular systematics at wikipedia
Cladistics at wikipedia
Tree of life web project
Tree of life - web based experiment
Embryology, Phylogenetics @ youtube
Parsimony - discussion and example
Affairs to remember - letter to the editor
Examples:Wooly Mammoth
Hominid phylogeny via Alu elements
Galapagos tortoises
Darwin's finches
Giraffes