########################################################################
##
##     DATA files for :
##
##      "Controlling for phylogenetic relatedness and evolutionary 
##      rates improves the discovery of associations between species'
##      phenotypic and genomic differences"
##
##      Xavier Prudent, Genis Parra, Peter Schwede, Juliana Roscito, Michael Hiller
##
##      Correponding author: Michael Hiller hiller@mpi-cbg.de
##
#######################################################################

#     Data for loss of Vitamin C synthesis

# All the genomic coordinates correspond to the Mouse GRCm38/mm10 genome assembly.

# The whole genome alignment can be found in the UCSC genome browser 
# as "Vertebrate Multiz Alignment & Conservation (60 Species)"


######################################
##
##  Conserved regions

# Phastcons data

phastcons.bed   # - Conserved elements from phastCons (bed format)
phastcons.bw    # - Conservation scores (big wig format) from phastCons


# GERP data

gerp.bed        # - Conserved elements from GERP (bed format)
gerp.bw         # - Conservation scores (big wig format) from GERP


# Final set of coding conserved regions 

conservedCDS.bed        # - Conserved coding regions (bed format)



######################################
##
##  Forward genomic data


# phylogenetic tree

tree.nh        # - in newick format


# percent identity values

global.CDS.percentID.txt      # - global percent identity data
local.CDS.percentID.txt       # - local percent identity data


# Forward genomics ouput:

forwardGenomics.output.txt              # - forward genomics results with all species
forwardGenomics.output.nopteVam1.txt    # - forward genomics results excluding the megabat (pteVam1)