#!/bin/sh -x

# To obtain the apomorphy list corresponding to the tree whose topology
# has been reconstructed by phyML
# paml uses the baseml.ctl file as the parameter file
baseml

# To perform the association test
# The outgroup must be sepcified for the association analysis (the tree 
# must be rooted). The outgroup is kept for the association test)
../../../../altree -i rst  -j nb_cas_control.txt  -a -t SNP \
--outgroup OUTG -p paml -r 1 -o 1_trio_ML.asso
