Various comp bio algorithms I've implemented.
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.
rabinkarp.java
is a Rabin-Karp algorithm implementation. Wiki link. Found in rabinkarp.java
.
Viterbi Algorithm. Wiki link. Found in viterbi.jl
.