relax SVN archive

The needleman_wunsch_align() function now accepts the end gap penalty arguments.

These are passed onto the needleman_wunsch_matrix() function.

Fix for the Needleman-Wunsch sequence alignment algorithm.

The start of the sequences are no longer truncated when starting gaps are encountered.

Created a unit test for demonstrating a failure in the Needleman-Wunsch sequence alignment algorithm.

The test is Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4b from the
_lib._sequence_alignment.test_needleman_wunsch module. The problem is that the start of the
alignment is truncated if any gaps are present.

Created the Test_needleman_wunsch.test_needleman_wunsch_align_NUC_4_4 unit test.

This is in the unit test module _lib._sequence_alignment.test_needleman_wunsch. This tests the
Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.

Modified the Test_needleman_wunsch.test_needleman_wunsch_align_DNA unit test to pass.

This is from the unit test module _lib._sequence_alignment.test_needleman_wunsch. The DNA sequences
were simplified so that the behaviour can be better predicted.

Added the PAM 250 amino acid substitution matrix.

This was taken from ftp://ftp.ncbi.nih.gov/blast/matrices/PAM250 and added to
lib.sequence_alignment.substitution_matrices.PAM250.

Added the header from ftp://ftp.ncbi.nih.gov/blast/matrices/BLOSUM62.

This is to document the BLOSUM62 substitution matrix.

Added the NUC 4.4 nucleotide substitution matrix from ftp://ftp.ncbi.nih.gov/blast/matrices/.

Uracil was added to the table as a copy to T.

Added sanity checks to the Needleman-Wunsch sequence alignment algorithm.

The residues of both sequences are now checked in needleman_wunsch_align() to make sure that they
are present in the substitution matrix.

Added a DNA similarity matrix to lib.sequence_alignment.substitution_matrices.