###NAK paper

###The following commands are based on the Exelixis Lab page hands on tutorial

###GAMMA run

###screen 27285

raxmlHPC -f c -s Dec23_12_NAKsequences_working.phy -m GTRGAMMA -n check_format

raxmlHPC -m GTRGAMMA -p 12345 -#200 -s Dec23_12_NAKsequences_working.phy -o mykissa2,mykissa3 -n ML_Dec30_G

raxmlHPC -m GTRGAMMA -p 12345 -b 12345 -#1000 -s Dec23_12_NAKsequences_working.phy -o mykissa2,mykissa3 -n BS_Dec30_G

raxmlHPC -m GTRGAMMA -p 12345 -f b -t  RAxML_bestTree.ML_Dec30_G -z RAxML_bootstrap.BS_Dec30_G -n Dec30_G

###GAMMAI run

###screen 28629

raxmlHPC -m GTRGAMMAI -p 12345 -#200 -s Dec23_12_NAKsequences_working.phy -o mykissa2,mykissa3 -n ML_Dec30_I

raxmlHPC -m GTRGAMMAI -p 12345 -b 12345 -#1000 -s Dec23_12_NAKsequences_working.phy -o mykissa2,mykissa3 -n BS_Dec30_I

raxmlHPC -m GTRGAMMAI -p 12345 -f b -t  RAxML_bestTree.ML_Dec30_I -z RAxML_bootstrap.BS_Dec30_I -n Dec30_I

###RAxML_bipartitions - support values assigned to nodes
###RAxML_bipartitionsBranchLabels - support values assigned to branches of the tree - Use with unrooted trees!

###Do a run without rooting the trees i.e. not assigning any outgroups;
###GAMMA run

###screen -r 9083

raxmlHPC -m GTRGAMMA -p 12345 -#200 -s Dec23_12_NAKsequences_working.phy -n ML_Dec30_GUnR

raxmlHPC -m GTRGAMMA -p 12345 -b 12345 -#1000 -s Dec23_12_NAKsequences_working.phy -n BS_Dec30_GUnR

raxmlHPC -m GTRGAMMA -p 12345 -f b -t  RAxML_bestTree.ML_Dec30_GUnR -z RAxML_bootstrap.BS_Dec30_GUnR -n Dec30_GUnR

###GAMMAI run

###screen -r 9140

raxmlHPC -m GTRGAMMAI -p 12345 -#200 -s Dec23_12_NAKsequences_working.phy -n ML_Dec30_IUnR

raxmlHPC -m GTRGAMMAI -p 12345 -b 12345 -#1000 -s Dec23_12_NAKsequences_working.phy -n BS_Dec30_IUnR

raxmlHPC -m GTRGAMMAI -p 12345 -f b -t  RAxML_bestTree.ML_Dec30_IUnR -z RAxML_bootstrap.BS_Dec30_IUnR -n Dec30_IUnR