[ { "id": "jmodeltest2", "name": "jmodeltest2", "article": "10.1080\/10635150390235520", "website": "https:\/\/github.com\/ddarriba\/jmodeltest2", "git": "https:\/\/github.com\/ddarriba\/jmodeltest2", "description": "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution", "version": "2.1.10", "documentation": "https:\/\/github.com\/ddarriba\/jmodeltest2\/files\/157130\/manual.pdf", "multiqc": "custom", "commands": [ { "name": "jmodeltest2", "cname": "jmodeltest2", "command": "java -jar $JMODELTEST_HOME\/jModelTest.jar", "category": "phylogenetics", "output_dir": "jmodeltest2", "inputs": [ { "name": "sequence_file", "type": [ "aligned_fasta", "phylip" ], "file": "", "description": "Sequence file", "from": "parameter" } ], "outputs": [ { "name": "model", "type": "txt", "file": "jmodeltest.out", "description": "Model file" } ], "options": [ { "name": "jmodeltest2_threads", "prefix": "-tr", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "jmodeltest2_sequence_file", "type": "input_file", "value": "", "label": "Path to sequence file" }, { "name": "jmodeltest2_confidence_interval", "prefix": "-c", "type": "numeric", "value": 100, "min": 0, "max": 100, "step": 1, "label": "Confidence interval" }, { "name": "jmodeltest2_AIC", "prefix": "-AIC", "type": "checkbox", "value": false, "label": "Calculate the Akaike Information Criterion" }, { "name": "jmodeltest2_AICc", "prefix": "-AICc", "type": "checkbox", "value": false, "label": "Calculate the corrected Akaike Information Criterion" }, { "name": "jmodeltest2_BIC", "prefix": "-BIC", "type": "checkbox", "value": false, "label": "Calculate the Bayesian Information Criterion" }, { "name": "jmodeltest2_DT", "prefix": "-DT", "type": "checkbox", "value": false, "label": "Calculate the decision theory criterion" }, { "name": "jmodeltest2_cat_number", "prefix": "-c", "type": "numeric", "value": 4, "min": "NA", "max": "NA", "step": 1, "label": "Include models with rate variation among sites and number of categories" }, { "name": "jmodeltest2_hLRTs_confidence_interval", "prefix": "-h", "type": "numeric", "value": 0.01, "min": "NA", "max": "NA", "step": "NA", "label": "Confidence level for the hLRTs" }, { "name": "jmodeltest2_hLRT", "prefix": "-hLRT", "type": "checkbox", "value": false, "label": "Do hierarchical likelihood ratio tests" }, { "name": "jmodeltest2_invar", "prefix": "-i", "type": "checkbox", "value": false, "label": "Include models with a proportion invariable sites" }, { "name": "jmodeltest2_treetopsearch", "prefix": "-S", "type": "select", "choices": [ { "NNI": "NNI" }, { "SPR": "SPR" }, { "BEST": "BEST" } ], "value": "BEST", "label": "Tree topology search operation option (NNI (fast), SPR (a bit slower), BEST (best of NNI and SPR))" }, { "name": "jmodeltest2_basetree", "prefix": "-t", "type": "select", "choices": [ { "fixed": "fixed" }, { "BIONJ": "BIONJ" }, { "ML": "ML" } ], "value": "ML", "label": "Base tree for likelihood calculations" }, { "name": "jmodeltest2_averaging", "prefix": "-v", "type": "checkbox", "value": false, "label": "Do model averaging and parameter importances" } ] } ], "install": { "apache_ant": [ "apt update -y", "apt install -y ant" ], "java8": [ "apt -y update", "apt install -y openjdk-8-jdk" ], "jmodeltest2": [ "ENV JMODELTEST_HOME \/opt\/biotools\/jmodeltest-2.1.10", "cd \/opt\/biotools", "wget https:\/\/github.com\/ddarriba\/jmodeltest2\/files\/157117\/jmodeltest-2.1.10.tar.gz", "tar -xvzf jmodeltest-2.1.10.tar.gz", "rm jmodeltest-2.1.10.tar.gz" ] }, "citations": { "jmodeltest2": [ "Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.", "Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704" ] }, "yaml": "{\n id: jmodeltest2,\n name: jmodeltest2 ,\n article: \"10.1080\/10635150390235520\",\n website: \"https:\/\/github.com\/ddarriba\/jmodeltest2\",\n git: \"https:\/\/github.com\/ddarriba\/jmodeltest2\",\n description: \"jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution\",\n version: \"2.1.10\",\n documentation: \"https:\/\/github.com\/ddarriba\/jmodeltest2\/files\/157130\/manual.pdf\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: jmodeltest2,\n cname: \"jmodeltest2\",\n command: \"java -jar $JMODELTEST_HOME\/jModelTest.jar\",\n category: \"phylogenetics\",\n output_dir: jmodeltest2,\n inputs: [{ name: sequence_file, type: [\"aligned_fasta\",\"phylip\"], file: \"\", description: \"Sequence file\", from: \"parameter\"}],\n outputs: [{ name: model, type: \"txt\", file: \"jmodeltest.out\", description: \"Model file\"}],\n options: [\n {\n name: jmodeltest2_threads,\n prefix: -tr,\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: jmodeltest2_sequence_file,\n type: input_file,\n value: \"\",\n label: \"Path to sequence file\",\n },\n {\n name: \"jmodeltest2_confidence_interval\",\n prefix: \"-c\",\n type: \"numeric\",\n value: 100,\n min: 0,\n max: 100,\n step: 1,\n label: \"Confidence interval\",\n },\n {\n name: jmodeltest2_AIC,\n prefix: -AIC,\n type: checkbox,\n value: FALSE,\n label: \"Calculate the Akaike Information Criterion\",\n },\n {\n name: jmodeltest2_AICc,\n prefix: -AICc,\n type: checkbox,\n value: FALSE,\n label: \"Calculate the corrected Akaike Information Criterion\",\n },\n {\n name: jmodeltest2_BIC,\n prefix: -BIC,\n type: checkbox,\n value: FALSE,\n label: \"Calculate the Bayesian Information Criterion\",\n },\n {\n name: jmodeltest2_DT,\n prefix: -DT,\n type: checkbox,\n value: FALSE,\n label: \"Calculate the decision theory criterion\",\n },\n {\n name: \"jmodeltest2_cat_number\",\n prefix: \"-c\",\n type: \"numeric\",\n value: 4,\n min: NA,\n max: NA,\n step: 1,\n label: \"Include models with rate variation among sites and number of categories\",\n },\n {\n name: \"jmodeltest2_hLRTs_confidence_interval\",\n prefix: \"-h\",\n type: \"numeric\",\n value: 0.01,\n min: NA,\n max: NA,\n step: NA,\n label: \"Confidence level for the hLRTs\",\n },\n {\n name: jmodeltest2_hLRT,\n prefix: -hLRT,\n type: checkbox,\n value: FALSE,\n label: \"Do hierarchical likelihood ratio tests\",\n },\n {\n name: jmodeltest2_invar,\n prefix: -i,\n type: checkbox,\n value: FALSE,\n label: \"Include models with a proportion invariable sites\",\n },\n {\n name: \"jmodeltest2_treetopsearch\",\n prefix: \"-S\",\n type: \"select\",\n choices:\n [\n NNI: \"NNI\",\n SPR: \"SPR\",\n BEST: \"BEST\",\n ],\n value: \"BEST\",\n label: \"Tree topology search operation option (NNI (fast), SPR (a bit slower), BEST (best of NNI and SPR))\",\n },\n {\n name: \"jmodeltest2_basetree\",\n prefix: \"-t\",\n type: \"select\",\n choices:\n [\n fixed: \"fixed\",\n BIONJ: \"BIONJ\",\n ML: \"ML\",\n ],\n value: \"ML\",\n label: \"Base tree for likelihood calculations\",\n },\n {\n name: jmodeltest2_averaging,\n prefix: -v,\n type: checkbox,\n value: FALSE,\n label: \"Do model averaging and parameter importances\",\n },\n ],\n },\n ],\n install:\n {\n apache_ant: [\n \"apt update -y\",\n \"apt install -y ant\"\n ],\n java8: [\n \"apt -y update\",\n \"apt install -y openjdk-8-jdk\"\n ],\n jmodeltest2: [\n \"ENV JMODELTEST_HOME \/opt\/biotools\/jmodeltest-2.1.10\",\n \"cd \/opt\/biotools\",\n \"wget https:\/\/github.com\/ddarriba\/jmodeltest2\/files\/157117\/jmodeltest-2.1.10.tar.gz\",\n \"tar -xvzf jmodeltest-2.1.10.tar.gz\",\n \"rm jmodeltest-2.1.10.tar.gz\",\n ]\n },\n citations:\n {\n jmodeltest2: [\n \"Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8), 772.\",\n \"Guindon S and Gascuel O (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704\" \n ]\n },\n}\n" } ]