Executable program is in the 'app' directory, a linux version and a macOS version, which you could directly download to use.
And source code is in the 'src' directory, which you could complie by yourself. Open the terminal, go to the './src' directory, run make
, the output executable program is in the 'bin' directory.
There are two ways to use this program.
One of the following scripts:
HSA <TreeS file path> <TreeT file path> <Cost file path> <g>
HSA <TreeS file path> <TreeT file path> <Cost file path> <l> <n>
HSA <TreeS file path> <TreeT file path> <Cost file path> <g> <testNum>
HSA <TreeS file path> <TreeT file path> <Cost file path> <l> <n> <testNum>
g: global alignment
l: local alignment
n: number of local alignments to output
testNum: number of test for calculate p-value (default:100, max:10000,min:2)
HSA [-h][--help]
-h: print short help and description
--help: print detailed help and description
HSA [-treeS <TreeS file path>][-treeT ] [-cost <Cost file path>]
[-method ] [-max_target <target num for l>]
[-test testNum] [-outfile <output file path>][-all ] [-prune pruneScore]
-treeS: TreeS file path
-treeT: TreeT file path
-cost: Cost file path. the cost file contains the score for different types of leaves
-method: l or g. g for global alignment; l for local alignment. default: g.
-max_target: target num for l, local alignment. default: 1
-test: testNum to calculate p-value. If testNum <=2, do not output p-value. default 0
-outfile: output file path. default: TreeS file path + l or g, based on -method
-all: T or F. output as much information as possible. default F;
-prune: pruneScore is the punish for pruning one leaf. default 1
./DELTA -treeS ./data/fun.alm -treeT ./data/fun.alm -cost ./data/cost.tsv -method l -test 100 -outfile DELTA_result -max target 10