[ { "id": "iqtree", "name": "IQ-TREE", "article": "10.1093\/molbev\/msu300", "website": "http:\/\/www.iqtree.org\/", "git": "https:\/\/github.com\/iqtree\/iqtree2", "description": "Efficient software for phylogenomic inference", "version": "2.2.2.7", "documentation": "http:\/\/www.iqtree.org\/doc\/", "multiqc": "custom", "commands": [ { "name": "iqtree", "cname": "iqtree", "command": "iqtree", "category": "phylogenetics", "output_dir": "iqtree", "inputs": [ { "name": "sequence_file", "type": [ "aligned_fasta", "phylip" ], "file": "", "description": "Sequence file", "from": "parameter" } ], "outputs": [ { "name": "treefile", "type": "newick", "file": "out.treefile", "description": "Tree file" }, { "name": "report", "type": "html", "file": "IQ-TREE_report_mqc.html", "description": "IQ-TREE report" } ], "options": [ { "name": "iqtree_threads", "prefix": "-nt", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "iqtree_sequence_file", "type": "input_file", "value": "", "label": "Path to sequence file" }, { "name": "iqtree_seed", "prefix": "-seed", "type": "numeric", "value": 1234, "min": "NA", "max": "NA", "step": "NA", "label": "Set the seed for the random number generator (use -1 for a random one)" }, { "name": "iqtree_model", "prefix": "-m", "type": "text", "value": "MFP", "label": "Model name (MFP automatically determines best-fit model before the tree inference; or choose one as described in http:\/\/www.iqtree.org\/doc\/Substitution-Models " }, { "name": "iqtree_bootstrap", "prefix": "", "type": "select", "choices": [ { "none": "none" }, { "Standard": "-b" }, { "Ultrafast": "-bb" } ], "value": "none", "label": "Use bootstrap analysis" }, { "name": "iqtree_bootstrap_val", "prefix": "", "type": "numeric", "value": 1000, "min": "NA", "max": "NA", "step": 1, "label": "Number of bootstrap alignments" }, { "name": "iqtree_partition_file", "type": "input_file", "value": "", "label": "Path to NEXUS partiton file" }, { "name": "iqtree_edge_status", "prefix": "", "type": "select", "choices": [ { "partitions share the same set of branch lengths": "-q" }, { "same set of branch lengths but partitions with own evolution rate": "-spp" }, { "each partition has its own set of branch lengths": "-sp" } ], "value": "none", "label": "estimate the model parameters separately for every partition ?" } ] } ], "install": [], "citations": { "iqtree": [ "L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https:\/\/doi.org\/10.1093\/molbev\/msu300" ] }, "yaml": "{\n id: iqtree,\n name: IQ-TREE ,\n article: \"10.1093\/molbev\/msu300\",\n website: \"http:\/\/www.iqtree.org\/\",\n git: \"https:\/\/github.com\/iqtree\/iqtree2\",\n description: \"Efficient software for phylogenomic inference\",\n version: \"2.2.2.7\",\n documentation: \"http:\/\/www.iqtree.org\/doc\/\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: iqtree,\n cname: \"iqtree\",\n command: \"iqtree\",\n category: \"phylogenetics\",\n output_dir: iqtree,\n inputs: [{ name: sequence_file, type: [\"aligned_fasta\",\"phylip\"], file: \"\", description: \"Sequence file\", from: \"parameter\"}],\n outputs: [\n { name: treefile, type: \"newick\", file: \"out.treefile\", description: \"Tree file\"},\n { name: report, type: \"html\", file: \"IQ-TREE_report_mqc.html\", description: \"IQ-TREE report\"}\n ],\n options: [\n {\n name: iqtree_threads,\n prefix: -nt,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: iqtree_sequence_file,\n type: input_file,\n value: \"\",\n label: \"Path to sequence file\",\n },\n {\n name: \"iqtree_seed\",\n prefix: \"-seed\",\n type: \"numeric\",\n value: 1234,\n min: NA,\n max: NA,\n step: NA,\n label: \"Set the seed for the random number generator (use -1 for a random one)\",\n },\n {\n name: \"iqtree_model\",\n prefix: \"-m\",\n type: text,\n value: \"MFP\",\n label: \"Model name (MFP automatically determines best-fit model before the tree inference; or choose one as described in http:\/\/www.iqtree.org\/doc\/Substitution-Models \",\n },\n {\n name: \"iqtree_bootstrap\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n none: \"none\",\n Standard: \"-b\",\n Ultrafast: \"-bb\",\n ],\n value: \"none\",\n label: \"Use bootstrap analysis\",\n },\n {\n name: \"iqtree_bootstrap_val\",\n prefix: \"\",\n type: \"numeric\",\n value: 1000,\n min: NA,\n max: NA,\n step: 1,\n label: \"Number of bootstrap alignments\",\n },\n {\n name: iqtree_partition_file,\n type: input_file,\n value: \"\",\n label: \"Path to NEXUS partiton file\",\n },\n {\n name: \"iqtree_edge_status\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n partitions share the same set of branch lengths: \"-q\",\n same set of branch lengths but partitions with own evolution rate: \"-spp\",\n each partition has its own set of branch lengths: \"-sp\",\n ],\n value: \"none\",\n label: \"estimate the model parameters separately for every partition ?\",\n },\n ],\n },\n ],\n install:\n {\n # iqtree: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/Cibiv\/IQ-TREE\/releases\/download\/v1.6.12\/iqtree-1.6.12-Linux.tar.gz\",\n # \"tar -xvzf iqtree-1.6.12-Linux.tar.gz\",\n # \"mv iqtree-1.6.12-Linux\/bin\/iqtree bin\/\",\n # \"rm -r iqtree-1.6.12-Linux iqtree-1.6.12-Linux.tar.gz\"\n # ]\n },\n citations:\n {\n iqtree: [\n \"L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https:\/\/doi.org\/10.1093\/molbev\/msu300\",\n ]\n },\n}\n" } ]