GcatWiki - User contributions [en]

MATH

2014-06-05T14:51:13Z

Kgutteridge:

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."
[https://sites.google.com/site/cbiomichael/software 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."
[http://statalign.github.io/index.html 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]]

'''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]]

File:Fishers Exact Test.ppt

2014-06-05T14:50:14Z

Kgutteridge:

File:Fisher’s Exact Test.pptx

2014-06-05T14:45:49Z

Kgutteridge:

MATH

2014-05-22T15:38:00Z

Kgutteridge:

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."
[https://sites.google.com/site/cbiomichael/software 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."
[http://statalign.github.io/index.html StatAlign link]

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

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