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data Tidied up Jul 27, 2018
.gitignore Include data files in repository Aug 23, 2015
2sum.py Tidied up Jul 27, 2018
ASMQ.py Passed ASMQ Sep 14, 2017
BA4M.py Solved PMCH Perfect Matchings and RNA Secondary Structures Oct 6, 2017
BA7A.py BA7A Compute Distances Between Leaves - solved Sep 21, 2017
BA7B.py Refactored some more common code Sep 26, 2017
BA7C.py started BA8E Implement Hierarchical Clustering Sep 26, 2017
BA7D.py Created skeltons for BA7E, BA7F, and BA7G Sep 26, 2017
BA7E.py Solved BA7E Implement the Neighbor Joining Algorithm Sep 27, 2017
BA7F.py Solved BA7G Adapt SmallParsimony to Unrooted Trees Sep 30, 2017
BA7G.py Solved BA7G Adapt SmallParsimony to Unrooted Trees Sep 30, 2017
BA8A.py Added copyright notice Sep 11, 2017
BA8B.py Coded, still testing Sep 20, 2017
BA8C.py Added copyright notice Sep 11, 2017
BA8D.py Added copyright notice Sep 11, 2017
BA8E.py Pass 1st test case Sep 26, 2017
BINS.py Added copyright notice Sep 11, 2017
CORR.py Started on DBRO. Moved revc into new utilit file rosalind.py Sep 11, 2017
DBRU.py DBRU now used stadard input function Sep 16, 2017
DDEG.py Added copyright notice Sep 11, 2017
DEG.py Added copyright notice Sep 11, 2017
FRMT.py Added copyright notice Sep 11, 2017
GASM.py Solved GASM Sep 13, 2017
GBK.py Added copyright notice Sep 11, 2017
GREP.py Extra doco Sep 16, 2017
INS.py Added copyright notice Sep 11, 2017
INV.py Added copyright notice Sep 11, 2017
KMP.py Started on ctbl Creating a Character Table Oct 1, 2017
LICENSE Initial commit Aug 23, 2015
LONG.py Added copyright notice Sep 11, 2017
MED.py Added copyright notice Sep 11, 2017
MER.py Added copyright notice Sep 11, 2017
MS.py Added copyright notice Sep 11, 2017
PAR.py Added copyright notice Sep 11, 2017
PAR3.py Added copyright notice Sep 11, 2017
PCOV.py GREP passes sample dataset test. Started moving input to rosalind.py Sep 16, 2017
PTRA.py Added copyright notice Sep 11, 2017
QS.py Added copyright notice Sep 11, 2017
README.md Solved 2SUM Jul 26, 2018
bfs.py Solved bfs Beadth First search Oct 7, 2017
cat.py Started bfs Beadth First search - 1st test case Oct 7, 2017
count-kmer-occurrences.py Tidied up Jul 27, 2018
cstr.py Additional doco Oct 5, 2017
ctbl.py Additional doco Oct 5, 2017
maj.py Tidied up Jul 27, 2018
mend.py Added copyright notice Sep 11, 2017
newick.py Solved NWCK (paths in trees Jul 19, 2017
nwck.py Added copyright notice Sep 11, 2017
pmch.py Comute Catalan Numbers Oct 7, 2017
rear.py Added copyright notice Sep 11, 2017
rosalind.py Comute Catalan Numbers Oct 7, 2017
rosalind.wpr Tidied up Jul 27, 2018

README.md

Bioinformatics

Code inspired by Finding Hidden Messages in DNA (Bioinformatics I) and from Rosalind. NB: functions generally used zero based indexing; Rodalind used 1-based.

Name Description
2sum.py 2SUM
ASMQ.py Assessing Assembly Quality with N50 and N75
BA4M.py Solve the Turnpike Problem
BA7A.py Compute Distances Between Leaves
BA7B.py Limb Length Problem
BA7C.py Implement Additive Phylogeny
BA7D.py Implement UPGMA
BA7E.py Implement the Neighbor Joining Algorithm
BA7F.py Implement SmallParsimony
BA7G.py Adapt SmallParsimony to Unrooted Trees
BA8A.py Implement FarthestFirstTraversal
BA8B.py Compute the Squared Error Distortion
BA8C.py Implement the Lloyd Algorithm for k-Means Clustering
BA8D.py Implement the Soft k-Means Clustering Algorithm
BA8E.py Implement Hierarchical Clustering
bfs.py Beadth First search !
BINS.py Binary Search
CORR.py Error Correction in Reads
count-kmer-occurrences.py Determine number of times each kmer appears in DNA, allowing for reverse complements and d-neighbourhoods
ctbl.py Creating a Character Table
DBRU.py Constructing a De Bruijn Graph
DDEG.py Double-Degree Array
DEG.py Degree Array
FRMT.py Data Formats
GASM.py Genome Assembly Using Reads
GBK.py GenBank Introduction
GREP.py Genome Assembly with Perfect Coverage and Repeats
INS.py Insertion Sort
INV.py Counting Inversions (WIP)
kmp.py Speeding Up Motif Finding
LICENSE License Agreement
LONG.py Genome Assembly as Shortest Superstring
maj.py Majority Element
MED.py Median
mend.py Inferring a Genotype from a Pedigree
MER.py Merge Two Sorted Arrays
MS.py Mergesort
newick.py
nwck.py Distances in Trees
PAR.py 2-Way Partition
PAR3.py 3-Way Partition
PCOV.py Genome Assembly with Perfect Coverage
pmch.py Perfect Matchings and RNA Secondary Structures
PTRA.py Protein Translation
QS.py Quicksort
README.md This file
rear.py Reversal distance
rosalind.py Shared code
rosalind.wpr WingWare Project File