Bioinformatics - genomics

source: Genomics/README.md

• Dealing with sequences
• Sequence repositories
• Metabarcoding
• Metagenomics
• Phylogenetics
  • Methods
  • Models
  • IQTREE
  • MrBayes

A quick overview on genomic resources

General resources

• Galaxy links - Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience.
  • Where to use galaxy
  • Galaxy tutorials
  • Galaxy Australia
• Australian BioComms and BioPlatforms - Australian centeric resources and community aimed at enhancing and training in all things big data.
• Pawsey Super Computing Centre - A Tier-1, High Performance Computing facility in Australia, whose primary function is to accelerate scientific research for the benefit of the nation.
• EMBL Australia - EMBL Australia is a life science network that supports ambitious research projects and provides access to infrastructure and training to early-career Australian scientists.

Resources for molecular phylogenetics

• Sydney Phylo Workshop by Simon Ho provides some excellent lecture notes and workshops with dataset
• Phylogenetic Biology by Casey Dunn at Brown University is a great source of lecture and practical material. It also has a an extensive list of extra resources and useful links to reading material
• RevBayes github page has a wealth of information specifically around the software but also includes some general phylogenetics material as well. Tutorial pages available here, a example of workshop page on molecular phylogenetics and fossil data available here
• Taming the BEAST workshops around the use of BEAST software for Phylogenetics
• Bayesian MCMC phylogenetics tutorial in R - for those wanting an R interface for their Phylogenetics
• Collection of tutorials on phylogenetics by Michael Matschiner. This goes through the workflow from sequence analysis through to dating and more
• Data Integration, Manipulation and Visualization of Phylogenetic Trees