copy_to_iqtree2_master.sh for synching with iqtree2 master branch.

Author: James Barbetti

copy_to_iqtree2_master.sh

@@ -0,0 +1,21 @@
+#!/bin/sh
+#Copies the current versions of files to iqtree2 (dev branch).
+#Opposite of decenttree_update.sh
+#  
+export DMT=../iqtree_master/distancematrixtree
+cp decenttree.cpp flatmatrix.cpp flatmatrix.h starttree.cpp starttree.h ${DMT}
+cp bionj.cpp bionj2.cpp bionj2.h upgma.h nj.h rapidnj.h auctionmatrix.h ${DMT}
+cp clustertree.h distancematrix.h stitchup.cpp sequence.cpp sequence.h  ${DMT}
+cp hashrow.h fancyrapidnj.h ${DMT}
+cd utils
+export UTILS=../../iqtree_master/utils
+cp argument.cpp argument.h               ${UTILS}
+cp gzstream.cpp gzstream.h heapsort.h    ${UTILS}
+cp progress.cpp progress.h               ${UTILS}
+cp operatingsystem.cpp operatingsystem.h ${UTILS}
+cp timeutil.h my_assert.h safe_io.h      ${UTILS}
+cp parallel_mergesort.h parallel_sort.h  ${UTILS}
+cp vectortypes.cpp vectortypes.h         ${UTILS}
+cp hammingdistance.h                     ${UTILS}
+cp stringfunctions.h stringfunctions.cpp ${UTILS}
+cd ..