#Install Bioedit
#Install notepad++
#Install Python2.7.9

#####################
# Branch-based test #
#####################

cd 0.Data\branch-based
..\..\1.prank\bin\prank.exe -d=GDPD4_cds.fa -o=GDPD4_MSA_cds -codon -F
# double click "reorder_ID.py"
..\..\2.Gblocks_0.91b\Gblocks.exe GDPD4_MSA_cds_reordered.fa -t=c
# open ctl files and check paths of seq, output, tree
..\..\3.paml4.9e\bin\codeml.exe GDPD4_H0.ctl > GDPD4_H0.report
..\..\3.paml4.9e\bin\codeml.exe GDPD4_H1.ctl > GDPD4_H1.report
#check results


####################
# Branch site test #
####################

cd 0.Data\branch-site
..\..\1.prank\bin\prank.exe -d=NCDN_cds.fa -o=NCDN_MSA_cds -codon -F
# double click "reorder_ID.py"
..\..\2.Gblocks_0.91b\Gblocks.exe NCDN_MSA_cds_reordered.fa -t=c
# copy output "NCDN_MSA_cds_reordered.fa-gb"
# change the name into "NCDN_MSA_cds_reordered.fa-gb_woOut.fa"
# delete IDs and sequences of outgroup species
# open ctl files and check paths of seq, output, tree
..\..\3.paml4.9e\bin\codeml.exe NCDN_H0.ctl > NCDN_H0.report
..\..\3.paml4.9e\bin\codeml.exe NCDN_H1.ctl > NCDN_H1.report
# check results
# double click "parsing_BEB.py"


#################
# TAAS analysis #
#################

# open "4.TAAS" folder
# run "TAAS.exe"
# write gene symbol
# copy sequences of targets and paste it upside blank
# copy sequences of others and paste it downside blank
# click run button
# check results