Phylogenomics workshop 2019:

  • Workshop practical - concatenation and gene partitioning
  • Wednesday's challenge - what yeast is in the brewery’s oak barrel?
  • Unaligned FASTA files
  • Aligned FASTA files
  • Aligned and trimmed FASTA files
  • Internode certainty and related measures

  • Coding:

  • UNIX Tutorial for Beginners
  • Command line challenge
  • Cyberciti's command line challenges
  • An introduction to R
  • Unix and perl oneliners for Bioinformatics
  • Bash loops

  • Statistics:

  • Biologist's guide to statistical thinking and analysis
  • Enrichment analysis
  • Multiple linear regression analysis in R
  • Kruskal-Wallis Test and associated post-hoc tests

  • Phylogenetics:

  • ALTER (ALingment Transformation EnviRonment)
  • CIPRES Science Gateway
  • Estimating diversification rates

  • Genomics:

  • The basics of SAMTools
  • Using CNVnator
  • Stepwise: R package for detecting recombination

  • Figure making:

  • Top 50 ggplot2 Visualizations
  • Visualize correlations
  • PCA/clustering visualization

  • Using ACCRE:

  • Lmod - loading modules
  • Example job array
  • Using Python on ACCRE