Develop a Python program that uses Dynamic Programming to compute the optimal alignment of two sequences.
It should meet the following conditions:
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The algorithm should read in two sequences (may be of different lengths) from text files.
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Initialise the scoring matrix and the backtracking matrix.
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Score each alignment using the following scores:
- +4 for a matching pair of ’A’ bases,
- +3 for a matching pair of ’C’ bases,
- +2 for a matching pair of ’G’ bases,
- +1 for a matching pair of ’T’ bases,
- -3 for a mismatching pair of bases,
- -2 for a gap.
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Use the backtracking matrix to determine an optimal alignment.
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The program should print out the following:
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The optimal alignment and its score.
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Execution times.
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Using the following matrix of inter-species distances, construct a phylogenetic tree using the UPGMA algorithm.
| a | b | c | d | e | f | |
|---|---|---|---|---|---|---|
| a | 0 | 15 | 24 | 29 | 25 | 37 |
| b | 15 | 0 | 32 | 31 | 23 | 43 |
| c | 24 | 32 | 0 | 30 | 43 | 49 |
| d | 29 | 31 | 30 | 0 | 45 | 57 |
| e | 25 | 23 | 43 | 45 | 0 | 55 |
| f | 37 | 43 | 49 | 57 | 55 | 0 |
Develop a Python program that uses the WPGMA algorithm to draw a phylogenetic tree from an input matrix of inter-species distances.
It should meet the following conditions:
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Your code should have a function called WPGMA which takes as its input the name of a text file.
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The algorithm should read in an inter-species distance matrix from this text file, and print this matrix to the screen.
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Follow the WPGMA algorithm, and print out to the screen every reduced distance matrix.
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After fully reducing the matrix, the code should draw the phylogentic tree obtained to a file. This tree does not need to contain edge weights.
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The program should print out the execution time to the screen.