#### Genome-wide patterns of sequence divergence of protein-coding genes between Drosophila buzzatii and D. mojavensis #####
Paper published in Journal of Heredity


Files and scripts for the protein coding genes divergence exploration in cactophilic Drosophila #

Authors: Yolanda Guillén, Sònia Casillas and Marta Coronado

CSV files:

divergence_table.csv

 Columns #
  parameter: dn, ds or omega #
  chr: Chromosome #
  position: bp position in Drosophila mojavensis #
  value: value of dn, ds or omega #
  length: Protein lenght (in aminoacids) in Drosophila buzzatii genome #
  Exons: Number of exons in Drosophila buzzatii genome #
  FBgn: Flybase gene ID #
  FBpp: Flybase protein ID #
  state: Gene located within a rearranged (1) or non-rearranged (0) segment considering fixed inversions #
  recomb: Gene located within non-recombining chromosome 6 and 3-Mb centromeric region (1) or in regions with presumably normal levels of recombination (0) #
  type: X-linked (1) or autosomal (0) region #
  breadth: Number of life stages (0-5) in which each gene is expressed using a minimu FPKM threshold of 1 #
  normexp: Maximum FPKM value observed across 5 life stages #

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divergence_window_100kb_table.csv #

Columns #
Position: Range non-overlapping window in Drosophila mojavensis. Position 1 refers to range (1-100kb), position 1000001 range (1001kb-200kb), etc. #
Chr: Chromosome #
variable: dn, ds or omega #
value: value of dn, ds or omega #

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R scripts:

code_divergence.R --> R script including regression models for dn, ds and omega parameters
plot_Figure_3.R --> R script to create Figure 3 from main paper