DELTA (Developmental Cell Lineage Tree Alignment)

DELTA is an novel computational framework for comparative analysis of developmental lineage trees reveals developmental motifs and their genetic basis.

Installation

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.

Method 1: the simple syntax

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)

Method 2: the verbose way

HSA [-h][--help]

-h: print short help and description

--help: print detailed help and description

Usage:

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]

Parameters description:

Required parameters:

-treeS: TreeS file path

-treeT: TreeT file path

-cost: Cost file path. the cost file contains the score for different types of leaves

Optional parameters:

-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

Example

./DELTA -treeS ./data/fun.alm -treeT ./data/fun.alm -cost ./data/cost.tsv -method l -test 100 -outfile DELTA_result -max target 10

yxj17173/DELTA