CompBio Algorithms

Various comp bio algorithms I've implemented.

Python

Dead End Elimination

Dead End Elimination is in dee.py. Wiki link. It can use two matrices, pair.dat and pair_small.dat. The file pair.dat is a plain text, tab-delimited file, containing the energies as a matrix of the following form:

E1    E12    E13  ...  E1N
0     E2     E23  ...  E2N
0     0      E3   ...  E3N
...  ...     ...  ...  ...
0     0       0   ...  EN

The file pair_small.dat is a smaller version of the same file in the same format.

Java

Rabin-Karp

rabinkarp.java is a Rabin-Karp algorithm implementation. Wiki link. Found in rabinkarp.java.

Julia

Viterbi

Viterbi Algorithm. Wiki link. Found in viterbi.jl.