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scripts/iq_tree_/change_genes_names_in_both_pal2nal_and_tree.sh

@@ -0,0 +1,3 @@
+pal2nal=$1
+tree=$2
+perl ~/Bin/inHouse/codeml_util/replace_gene_tree_and_alignment_with_same_names.pl  $pal2nal $tree

scripts/iq_tree_/change_iqGeneTree_to_old_names.sh

@@ -0,0 +1,7 @@
+tree=$1
+#perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/,/\n,/g;  print $_;' $tree | sed 's/_/|/' | perl -ne 'chomp; s/\)\d+/\)/g; print $_;' > ${tree/.**}.original_names.tre  
+
+#same as:perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/,/\n,/g; s/\)\d+/\)/g;  print $_;' $tree | sed 's/_/|/' | perl -ne 'chomp; print $_;' > 
+
+
+sed 's/,/\n/g' $tree | sed 's/_/\|/'| perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/\n/,/;print $_;' |perl -pe 's/,$//;' > ${tree/.**}.original_names.tre 

scripts/iq_tree_/change_orthofinder.tree.2.original.names.sh

@@ -0,0 +1,8 @@
+tree=$1
+#perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/,/\n,/g;  print $_;' $tree | sed 's/_/|/' | perl -ne 'chomp; s/\)\d+/\)/g; print $_;' > ${tree/.**}.original_names.tre  
+
+#same as:perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/,/\n,/g; s/\)\d+/\)/g;  print $_;' $tree | sed 's/_/|/' | perl -ne 'chomp; print $_;' > 
+
+
+
+sed 's/,/\n/g'  $tree | perl -ne 's/_\S+\|/\|/g; print $_;' | perl -ne 's/\)\d*:\d*\.\d*/\)/g; s/:\d*\.\d*//g; s/\n/,/;print $_;' > ${tree/_**}.original_names.tre