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Beyond_Prompt-based_Retrieval

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Beyond_Prompt-based_Retrieval
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{
	"tools": [
		{
			"name": "PLINK 2.0",
			"function_name": "install_plink2",
			"description": "Whole genome association analysis toolset",
			"website": "https://www.cog-genomics.org/plink/2.0/",
			"downloads": {
				"linux": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_linux_avx2_20250129.zip",
				"macos_intel": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_mac_avx2_20250129.zip",
				"macos_arm64": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_mac_arm64_20250129.zip"
			},
			"binary_path": "plink2",
			"version_command": "--version"
		},
		{
			"name": "IQ-TREE",
			"function_name": "install_iqtree",
			"description": "Efficient phylogenetic software by maximum likelihood",
			"website": "http://www.iqtree.org/",
			"downloads": {
				"linux": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz",
				"macos_intel": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-MacOSX.zip",
				"macos_arm64": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-MacOSX.zip"
			},
			"binary_path": "bin/iqtree2",
			"version_command": "--version"
		},
		{
			"name": "GCTA",
			"function_name": "install_gcta",
			"description": "Genome-wide Complex Trait Analysis",
			"website": "https://yanglab.westlake.edu.cn/software/gcta/",
			"downloads": {
				"linux": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.4-linux-kernel-3-x86_64.zip",
				"macos_intel": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.1-macOS-x86_64.zip",
				"macos_arm64": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.3-macOS-arm64.zip"
			},
			"binary_path": "gcta64",
			"version_command": ""
		},
		{
			"name": "BWA",
			"function_name": "install_bwa",
			"description": "Burrow-Wheeler Aligner for short-read alignment",
			"website": "https://github.com/lh3/bwa",
			"downloads": {
				"linux": "https://github.com/lh3/bwa.git",
				"macos_intel": "https://github.com/lh3/bwa.git",
				"macos_arm64": "https://github.com/lh3/bwa.git"
			},
			"binary_path": "bwa",
			"version_command": ""
		},
		{
			"name": "FastTree",
			"function_name": "install_fasttree",
			"description": "Approximately-Maximum-Likelihood phylogenetic trees from alignments",
			"website": "https://morgannprice.github.io/fasttree/",
			"downloads": {
				"linux": "https://morgannprice.github.io/fasttree/FastTree.c",
				"macos_intel": "https://morgannprice.github.io/fasttree/FastTree.c",
				"macos_arm64": "https://morgannprice.github.io/fasttree/FastTree.c"
			},
			"binary_path": "FastTree",
			"version_command": "-help | head -n 2"
		},
		{
			"name": "MUSCLE",
			"function_name": "install_muscle",
			"description": "Multiple sequence alignment with high accuracy and performance",
			"website": "https://github.com/rcedgar/muscle",
			"downloads": {
				"linux": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-linux-x86.v5.3",
				"macos_arm64": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-osx-arm64.v5.3"
			},
			"binary_path": "muscle",
			"version_command": "-version"
		},
		{
			"name": "HOMER",
			"function_name": "install_homer",
			"description": "Software for motif discovery and next-gen sequencing analysis",
			"website": "http://homer.ucsd.edu/homer/",
			"downloads": {
				"linux": "http://homer.ucsd.edu/homer/configureHomer.pl",
				"macos_intel": "http://homer.ucsd.edu/homer/configureHomer.pl",
				"macos_arm64": "http://homer.ucsd.edu/homer/configureHomer.pl"
			},
			"binary_path": "bin/findMotifs.pl",
			"version_command": "-h"
		}
	]
}