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.gitignore Include data files in repository Aug 23, 2015 Tidied up Jul 27, 2018 Refactored some more common code Sep 26, 2017 started BA8E Implement Hierarchical Clustering Sep 26, 2017 Added copyright notice Sep 11, 2017 Started on DBRO. Moved revc into new utilit file Sep 11, 2017 Added copyright notice Sep 11, 2017 Solved GASM Sep 13, 2017 Extra doco Sep 16, 2017
LICENSE Added copyright notice Sep 11, 2017 Added copyright notice Sep 11, 2017 GREP passes sample dataset test. Started moving input to Sep 16, 2017 Solved 2SUM Jul 26, 2018 Tidied up Jul 27, 2018 Additional doco Oct 5, 2017 Added copyright notice Sep 11, 2017


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 Assessing Assembly Quality with N50 and N75 Solve the Turnpike Problem Compute Distances Between Leaves Limb Length Problem Implement Additive Phylogeny Implement UPGMA Implement the Neighbor Joining Algorithm Implement SmallParsimony Adapt SmallParsimony to Unrooted Trees Implement FarthestFirstTraversal Compute the Squared Error Distortion Implement the Lloyd Algorithm for k-Means Clustering Implement the Soft k-Means Clustering Algorithm Implement Hierarchical Clustering Beadth First search ! Binary Search Error Correction in Reads Determine number of times each kmer appears in DNA, allowing for reverse complements and d-neighbourhoods Creating a Character Table Constructing a De Bruijn Graph Double-Degree Array Degree Array Data Formats Genome Assembly Using Reads GenBank Introduction Genome Assembly with Perfect Coverage and Repeats Insertion Sort Counting Inversions (WIP) Speeding Up Motif Finding
LICENSE License Agreement Genome Assembly as Shortest Superstring Majority Element Median Inferring a Genotype from a Pedigree Merge Two Sorted Arrays Mergesort Distances in Trees 2-Way Partition 3-Way Partition Genome Assembly with Perfect Coverage Perfect Matchings and RNA Secondary Structures Protein Translation Quicksort This file Reversal distance Shared code
rosalind.wpr WingWare Project File