Bioinformatics Institute
Software tools
Bioinformatics Institute staff, students, and affiliates have contributed to the development of many resources, listed below.
| Tool name | Contact person | Date updated |
|---|---|---|
| BEAST2 | BEAST users group | Frequently |
| DNA Surveillance | dna-surveillance@auckland.ac.nz | 2012 |
| DTWave | Louis Ranjard | 2016 |
| DTWave_cluster | Louis Ranjard | 2016 |
| GeneSetDB | bioinformatics@auckland.ac.nz | 2013 |
| MelanomaDB | bioinformatics@auckland.ac.nz | 2013 |
| Melanoma Profiler | bioinformatics@auckland.ac.nz | 2014 |
| Pebble | Matthew Goode | 2004 |
| Phyloland | Louis Ranjard | 2014 |
| PhyML | Stephane Guindon | 2012 |
| shiny_cuffdiff | Dan Jones |
2016 |
| Species Delimitation plugin for Geneious | Howard Ross | 2014 |
| SplitsTree4 | David Bryant | 2006 |
| Squint | Matthew Goode | 2007 |
BEAST2
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. This tool was developed through a collaborative project by Professor Alexei Drummond.
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DNA Surveillance
DNA Surveillance is a system used for the identification of species using phylogenetic analyses
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DTWave
DTWave is a tool for analysis of sound sequences. It was developed by Dr Louis Ranjard.
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DTWave_cluster - Unsupervised Sound Classification using Artificial Neural Network
DTWave_cluster performs automatic classification of a set of WAV sound files. Typically, DTWave_cluster can be used for the automatic classification of any bioacoustics signal when no prior information about clustering is available. It relies on the C program DTWave (DTWave) for sound alignment and average computation and uses an unsupervised artificial neural network clustering algorithm.
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GeneSetDB
GeneSetDB is a comprehensive meta-database with associated gene set enrichment analysis statistical tools, which integrates a large number of other biological databases for gene set analysis.
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MelanomaDB
MelanomaDB is a web interface to a large database of melanoma genomic information. It is a specific application of the GeneSetDB web tool. Using MelanomaDB, users can identify the intersection and union between sets of genes including personal lists of genes.
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Melanoma Profiler
Melanoma Profiler is a web application for cancer genomic research which is accessed through Illumina's BaseSpace portal. It performs a comparative variant analysis across tumor and germline samples, comparing modified genes and pathways to those in a curated set of known melanoma tumor samples.
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Pebble
Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a phylogenetic analysis application which provides tools for analysis and simulation of serially sampled sequence data. It was developed by Professor Allen Rodrigo and Matthew Goode.
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Phyloland
The R package Phyloland implements a model of space colonization mapped onto a phylogeny, it aims at testing for limited dispersal and ecological competitive exclusion in a Bayesian MCMC statistical phylogeographic framework.
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PhyML
PhyML is a phylogeny software based on the maximum-likelihood principle. This tool was developed through a collaborative project by Dr Stephane Guindon.
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shiny_cuffdiff
shiny_cuffdiff is a Shiny/R interface used to visualise the outputs from the Tuxedo workflow (Tophat2 > Cufflinks > Cuffdiff), which is a cuffdiff SQL database. Plots are created using the gene names or XLOC number.
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Species Delimitation plugin for Geneious
The Species Delimitation plugin for the Geneious bioinformatics software is an exploratory tool that allows users to assess putative species in phylogenetic trees.
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SplitsTree4
SplitsTree4 is an application for computing unrooted phylogenetic networks from molecular sequence data.
