molecular evo info

test/ctl_files/t1_ebola_preads.ctl

@@ -16,20 +16,24 @@
          data = 4  # *See below 0:only complete(F); 1:only contig(C); 2:only reads(R); 
                    # 3:combination F+C; 4:combination F+R; 5:combination C+R; 
                    # 6:combination F+C+R; 7:realignment  *See below 
+
         reads = 2  # 1: single reads; 2: paired reads; 3: both types present;
+
+        SNPsfilter = 0.6 #
 
-         tree = 1  # 0:no tree; 1:use FastTree; 2:use RAxML; 3:use both;
+         tree = 4  # 0:no tree; 1:use FastTree; 2:use RAxML; 3:use IQ tree 4:all;
     bootstrap = 0  # 0:no; 1:yes;  # Run bootstrapping  *See below
-            N = 10  # Number of bootstraps to run *See below    
+            N = 0  # Number of bootstraps to run *See below    
 
-    PosSelect = 1  # 0:No; 1:use PAML; 2:use HyPhy; 3:use both
+    PosSelect = 0  # 0:No; 1:use PAML; 2:use HyPhy; 3:use both
 
          code = 1  # 0:Bacteria; 1:Virus
 
-        clean = 0  # 0:no clean; 1:clean
+        clean = 1  # 0:no clean; 1:clean
 
       threads = 2  # Number of threads to use
 
-       cutoff = 0.0  # Linear alignment (LA) coverage against reference - ignores SNPs from organism that have lower cutoff.
+       cutoff = 0.5  # Linear alignment (LA) coverage against reference - ignores SNPs from organism that have lower cutoff.
+