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e33876c2e1
Adds a new CodonAligner class to Bio.Align. This class has the same capabilities as the codon aligner in Bio.codonalign, but instead of regular expressions, it uses a dynamic programming algorithm based on the pairwise aligner in Bio.Align. Also adds a mapall method to the Alignment class. When applied to a protein alignment, with a list of nucleotide-to-protein alignments generated using the CodonAligner, it will return a nucleotide alignment where codons are aligned to each other. The analysis methods calculate_dn_ds, calculate_dn_ds_matrix, and mktest are provided in a new submodule Bio.Align.analysis, acting on an Alignment object containing a nucleotide alignment of codons. I believe that with this PR, Bio.codonalign can be deprecated (to be done later in a separate PR). This PR also fixes issue #4466. As an aside, the sorts the bibliography entries in the Tutorial.