MATH

Nava: "NAVA is a tool for visualising and analysing annotated secondary structures of large single-stranded RNA or DNA sequences (such as full-length virus genomes). The purpose of this tool is to assist investigators in evaluating the biological relevance of RNA or DNA secondary structures within particular sequences." Nava Link

StatAlign: "StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. A broad range of models for nucleotide and amino acid data is included in the package and the plug-in management system ensures that new models can be easily added." StatAlign link

UNAFold: "UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction."

Statistics work: File:Statistics ChiSquared.xlsx

Excel File for Calculation of Probabilities of Sampling Error: File:Sample Probabilities.xlsx

Fisher's Exact Test File:Fishers Exact Test.ppt

Caffeine Experiment Results Statistics: File:Caffeine Results.pptx

Markov Chains:

An introduction to Markov Chains and Hidden Markov Models. File:Markov Chains.pptx

Hidden Markov Models File:HiddenMarkovModels.pdf

A Presentation on Hidden Markov Models: File:Hidden Markov Models.pptx