bootstrap gene trees

Author: tkchafin

bootstrapGeneTrees.sh

@@ -0,0 +1,21 @@
+#!/bin/bash 
+
+#Tyler K. Chafin 
+#July 23 2021
+#Generates n bootstrap samples of an input newick-formatted file of trees
+#Email: [email protected] with issues
+
+if [ $1 ] && [ $2 ]; 
+then 
+  trees="$1"
+  n=$2
+else 
+  printf "\nUsage: $0 <tree file> <n>\n\n"
+  exit 1
+fi
+
+for i in `seq 1 $n`; 
+do
+  ofile="b_"$i".tre"
+  shuf -r -n $n $trees > $ofile
+done

test_files/gtrees.tre

@@ -0,0 +1,10 @@
+(4,(1,(2,3)));
+(4,(2,(1,3)));
+(4,(1,(2,3)));
+(4,(2,(1,3)));
+(1,(4,(2,3)));
+(4,(3,(2,3)));
+(4,(2,(1,3)));
+(4,(1,(2,3)));
+(4,(2,(1,3)));
+(1,(4,(2,3)));