Software Tools :: Phylogenetic Analysis
The programs in this section are used to investigate the evolutionary history
of organisms based on their DNA or protein sequences. Most of these analyses
require a multiple sequence alignment as the starting point, and the results
are dependent on the quality of the alignment. Multiple sequence alignment
programs are designed to produce an alignment that is mathematically
correct for the given program parameters; this alignment may not be
biologically correct. For example, alignments of nucleic acid sequences
that code for proteins may contain gaps inserted within codons. It is crucial
for you to examine any computer-generated alignment carefully and to adjust it
by hand if necessary to make sure the final alignment makes biological sense.
Tree reconstruction
There are three types of methods used to reconstruct evolutionary trees:
distance methods, parsimony methods, and maximum likelihood methods.
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Phylogenetic Analysis
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