diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/all_forams.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/all_forams.txt
new file mode 100644
index 0000000..32be151
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/all_forams.txt
@@ -0,0 +1,45 @@
+Sr_rh_ArpA
+Sr_rh_As01
+Sr_rh_As11
+Sr_rh_As25
+Sr_rh_AspA
+Sr_rh_Bost
+Sr_rh_Bspi
+Sr_rh_Bv01
+Sr_rh_Bv03
+Sr_rh_Calb
+Sr_rh_Cosp
+Sr_rh_El02
+Sr_rh_Emac
+Sr_rh_Emar
+Sr_rh_Esca
+Sr_rh_Gl02
+Sr_rh_Gpac
+Sr_rh_Gsp1
+Sr_rh_Hg01
+Sr_rh_HgpA
+Sr_rh_Hhir
+Sr_rh_Hind
+Sr_rh_Lvor
+Sr_rh_Mf01
+Sr_rh_Mf02
+Sr_rh_Nn01
+Sr_rh_Nn10
+Sr_rh_Pbet
+Sr_rh_Ph16
+Sr_rh_Ph19
+Sr_rh_Ph24
+Sr_rh_PspA
+Sr_rh_Qj01
+Sr_rh_QjpA
+Sr_rh_RspA
+Sr_rh_Slin
+Sr_rh_Spsu
+Sr_rh_Ss02
+Sr_rh_Ss03
+Sr_rh_Tr01
+Sr_rh_Tr02
+Sr_rh_Ts02
+Sr_rh_Tsp1
+Sr_rh_Tx01
+Sr_rh_Ustr
diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/cercozoa.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/cercozoa.txt
new file mode 100644
index 0000000..96f6b17
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/cercozoa.txt
@@ -0,0 +1,9 @@
+Sr_rh_Gspa
+Sr_rh_Lamo
+Sr_rh_Blon
+Sr_rh_Bna2
+Sr_rh_Crep
+Sr_rh_Nsph
+Sr_rh_Pglo
+Sr_rh_Erot
+Sr_rh_Pami
diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/clade_grabbing_rules.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/clade_grabbing_rules.txt
new file mode 100644
index 0000000..6c46028
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/clade_grabbing_rules.txt
@@ -0,0 +1,23 @@
+Am	0.1	11	NA	0
+Am_ar	0	3	NA	0
+Am_di	0	3	NA	0
+Am_my	0	4	NA	0
+Am_tu	0.1	7	NA	0
+EE_cr	0.1	11	NA	0
+EE_ha	0.1	9	NA	0
+Ex	0.1	8	NA	0
+Ex_eu	0.1	9	NA	0
+Ex_fo	0	3	NA	0
+Ex_pa	0	3	NA	0
+Op	0.1	11	NA	0
+Op_fu	0.1	11	NA	0
+Op_me	0.1	11	NA	0
+Pl_gl	0	3	NA	0
+Pl_gr	0.1	13	NA	0
+Pl_rh	0.1	9	NA	0
+Sr_ap	0.1	6	NA	0
+Sr_ci	0.1	13	lkh_ciliates.txt	1
+Sr_di	0.1	11	NA	0
+Sr_st	0.1	11	NA	0
+Sr_rh	0.1	7	cercozoa.txt	5
+all_forams.txt	0.1	11	lkh_forams.txt	1
diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/exceptions.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/exceptions.txt
new file mode 100644
index 0000000..b216a70
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/exceptions.txt
@@ -0,0 +1,21 @@
+Am_ev
+Am_is
+Am_th
+EE_an
+EE_ap
+EE_br
+EE_ce
+EE_is
+EE_pr
+EE_rh
+Ex_is
+Ex_ja
+Ex_ma
+Ex_me
+Ex_ox
+Op_ap
+Op_ic
+Op_nu
+Sr_ch
+Sr_co
+Sr_pe
diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_ciliates.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_ciliates.txt
new file mode 100644
index 0000000..f543600
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_ciliates.txt
@@ -0,0 +1,12 @@
+Sr_ci_Tp05
+Sr_ci_Ty13
+Sr_ci_Si09
+Sr_ci_Sc02
+Sr_ci_Eu04
+Sr_ci_Tn01
+Sr_ci_Hx49
+Sr_ci_Sx06
+Sr_ci_Sa01
+Sr_ci_Lx03
+Sr_ci_Lx74
+Sr_ci_Ls01
diff --git a/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_forams.txt b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_forams.txt
new file mode 100644
index 0000000..9ba17b6
--- /dev/null
+++ b/PTL2/Examplar_runs/Running_CLoop/CladeGrabbing/lkh_forams.txt
@@ -0,0 +1,22 @@
+Sr_rh_AspA
+Sr_rh_RspA
+Sr_rh_Mf01
+Sr_rh_Mf02
+Sr_rh_Qj01
+Sr_rh_QjpA
+Sr_rh_Tr01
+Sr_rh_Tr02
+Sr_rh_Ss02
+Sr_rh_Ss03
+Sr_rh_ArpA
+Sr_rh_Ph16
+Sr_rh_Ph19
+Sr_rh_Ph24
+Sr_rh_PspA
+Sr_rh_El02
+Sr_rh_Hg01
+Sr_rh_HgpA
+Sr_rh_As01
+Sr_rh_As11
+Sr_rh_As25
+Sr_rh_Ts02