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3.between_species

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3.between_species [2017/12/15 15:41] – created hyjeong3.between_species [2021/03/17 13:09] (current) – external edit 127.0.0.1
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   #Install Bioedit   #Install Bioedit
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   #Install notepad++   #Install notepad++
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   #Install Python2.7.9   #Install Python2.7.9
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   #####################   #####################
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   # Branch-based test #   # Branch-based test #
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   #####################   #####################
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   cd 0.Data\branch-based   cd 0.Data\branch-based
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   ..\..\1.prank\bin\prank.exe -d=GDPD4_cds.fa -o=GDPD4_MSA_cds -codon -F   ..\..\1.prank\bin\prank.exe -d=GDPD4_cds.fa -o=GDPD4_MSA_cds -codon -F
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   # double click "reorder_ID.py"   # double click "reorder_ID.py"
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   ..\..\2.Gblocks_0.91b\Gblocks.exe GDPD4_MSA_cds_reordered.fa -t=c   ..\..\2.Gblocks_0.91b\Gblocks.exe GDPD4_MSA_cds_reordered.fa -t=c
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   # open ctl files and check paths of seq, output, tree   # open ctl files and check paths of seq, output, tree
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   ..\..\3.paml4.9e\bin\codeml.exe GDPD4_H0.ctl > GDPD4_H0.report   ..\..\3.paml4.9e\bin\codeml.exe GDPD4_H0.ctl > GDPD4_H0.report
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   ..\..\3.paml4.9e\bin\codeml.exe GDPD4_H1.ctl > GDPD4_H1.report   ..\..\3.paml4.9e\bin\codeml.exe GDPD4_H1.ctl > GDPD4_H1.report
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   #check results   #check results
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   ####################   ####################
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   # Branch site test #   # Branch site test #
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   ####################   ####################
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   cd 0.Data\branch-site   cd 0.Data\branch-site
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   ..\..\1.prank\bin\prank.exe -d=NCDN_cds.fa -o=NCDN_MSA_cds -codon -F   ..\..\1.prank\bin\prank.exe -d=NCDN_cds.fa -o=NCDN_MSA_cds -codon -F
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   # double click "reorder_ID.py"   # double click "reorder_ID.py"
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   ..\..\2.Gblocks_0.91b\Gblocks.exe NCDN_MSA_cds_reordered.fa -t=c   ..\..\2.Gblocks_0.91b\Gblocks.exe NCDN_MSA_cds_reordered.fa -t=c
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   # copy output "NCDN_MSA_cds_reordered.fa-gb"   # copy output "NCDN_MSA_cds_reordered.fa-gb"
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   # change the name into "NCDN_MSA_cds_reordered.fa-gb_woOut.fa"   # change the name into "NCDN_MSA_cds_reordered.fa-gb_woOut.fa"
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   # delete IDs and sequences of outgroup species   # delete IDs and sequences of outgroup species
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   # open ctl files and check paths of seq, output, tree   # open ctl files and check paths of seq, output, tree
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   ..\..\3.paml4.9e\bin\codeml.exe NCDN_H0.ctl > NCDN_H0.report   ..\..\3.paml4.9e\bin\codeml.exe NCDN_H0.ctl > NCDN_H0.report
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   ..\..\3.paml4.9e\bin\codeml.exe NCDN_H1.ctl > NCDN_H1.report   ..\..\3.paml4.9e\bin\codeml.exe NCDN_H1.ctl > NCDN_H1.report
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   # check results   # check results
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   # double click "parsing_BEB.py"   # double click "parsing_BEB.py"
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   #################   #################
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   # TAAS analysis #   # TAAS analysis #
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   #################   #################
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   # open "4.TAAS" folder   # open "4.TAAS" folder
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   # run "TAAS.exe"   # run "TAAS.exe"
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   # write gene symbol   # write gene symbol
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   # copy sequences of targets and paste it upside blank   # copy sequences of targets and paste it upside blank
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   # copy sequences of others and paste it downside blank   # copy sequences of others and paste it downside blank
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   # click run button   # click run button
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   # check results   # check results
  
3.between_species.1513320079.txt.gz · Last modified: (external edit)