voutcn / FP-COMP8503

Codes and files for the final project of COMP8503

Results

• Average linkage
• Complete linkage
• Single linkage: the best one

Reproducing the results

Step 1: clone the repo

git clone https://github.com/voutcn/FP-COMP8503.git && cd FP-COMP8503

Step 2: compile

g++ -O2 to_vector.cpp -o to_vector -lz
g++ -O2 cluster.cpp -o cluster -static-libstdc++ -std=c++0x -lz

Step 3: spilt genome

for i in `ls *.fna`; do src/to_vector $i >> data100k.txt; done

Step 4: do clustering

./cluster data100k.txt 0 > avg.tree
./cluster data100k.txt 1 > cmp.tree
./cluster data100k.txt 2 > sng.tree

Step 5: visualize the tree

Upload avg.tree, cmp.tree and sng.tree to http://www.hiv.lanl.gov/content/sequence/RAINBOWTREE/rainbowtree.html. In the "Option" tags, choose

"Color tree according to the column in field 1 of sequence names delimited by _".