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This repository contains the realization of the project "Phylogeny" for the course of bioinformatics 2.

The Introduction section briefly describes the module phylogeny with its main classes, in the section Features are described in detail all implemented aspects. See Tutorial section for how to use them. To carry out the project it was necessary to correct some bugs in the Align2 package and extend it, all can be found in the section Victor changes.

Note: ClustalW2 is a great heuristic and many of the current features are not documented in the original doc CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. To improve the result some of this features are obtained by sifting through evidence and reverse engineering, for details see Differences with ClustalW2.