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Tutorial_GenomeEvolution

Genome Evolution Lecture for Phylogenomics Workshop

Framework for learning some basic Evolutionary Genomics and Comprative steps

Requirements:

  • R
  • R packages “ggplot2”,”gridExtra”,”dplyr”,”RColorBrewer”, "pheatmap"
  • R/Bioconductor packages AnnotationDbi and tximport
  • install these packages with Rscript scripts/install_pkg.R

Data

  • there are data in the data folder and you should run download.sh for an example of how to download data from FungiDB data/dna_species.dat lists the names of the species to download. These are the prefixes for the files in this folder at FungiDB http://fungidb.org/common/downloads/Current_Release/ - note you want the name of folders which list the strain eg Umaydis521 not Umaydis which is where the genome data are located.

  • pre-run OrthoFinder results are in analysis/ortho_set1/Results see the Orthogroups.csv and Orthogroups.GeneCount.csv for orthologs contain See the Orthogroups_UnassignedGenes.csv for genes which are not in a cluster

scripts

  • plot_chroms_1.R is an R script to generate some summary graphics from GFF files
  • plot_heatmap_family.R is an R script to generate a heat map for gene family sizes
  • extract_orthologs_single-copy_Afum.py is a python script to

Run the R script Rscript scripts/plot_chroms_1.R

  • see the output in plots Rscript scripts/plot_heatmap_family.R
  • see output in plots - also walk through each line one at a time in Rstudio or elsewhere

run the pythonscript to see how to extract gene families which are single-copy for the two Afumigatus strains ./scripts/extract_orthologs_single-copy_Afum.py

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