[ { "id": "raxml_ng", "name": "RAxML-NG", "article": "10.1093\/bioinformatics\/btz305", "website": "https:\/\/github.com\/amkozlov\/raxml-ng", "git": "https:\/\/github.com\/amkozlov\/raxml-ng", "description": "RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion", "version": "1.2.0", "documentation": "https:\/\/github.com\/amkozlov\/raxml-ng\/wiki", "multiqc": "custom", "commands": [ { "name": "raxml_ng", "cname": "raxml_ng", "command": "raxml-ng", "category": "phylogenetics", "output_dir": "raxml_ng", "inputs": [ { "name": "aligned_seqs", "type": [ "aligned_fasta", "phylip" ], "description": "Aligned sequences", "from": "parameter" } ], "outputs": [ { "name": "best_tree", "type": "newick", "file": "run.raxml.bestTree", "description": "Best-scoring ML tree (strictly bifurcating)" }, { "name": "log", "type": "txt", "file": "run.raxml.log", "description": "RAxML-NG log" } ], "options": [ { "name": "raxml_ng_threads", "prefix": "--threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "raxml_ng_seed", "prefix": "--seed", "type": "numeric", "value": 1234, "min": 0, "max": "NA", "step": 1, "label": "seed for pseudo-random number generator" }, { "name": "raxml_ng_aligned_seqs", "type": "input_file", "value": "", "label": "Path to aligned sequences file" }, { "name": "raxml_ng_model_name", "prefix": "--model", "type": "select", "choices": [ { "JC": "JC" }, { "K80": "K80" }, { "F81": "F81" }, { "HKY": "HKY" }, { "TN93ef": "TN93ef" }, { "TN93": "TN93" }, { "K81": "K81" }, { "K81uf": "K81uf" }, { "TPM2": "TPM2" }, { "TPM2uf": "TPM2uf" }, { "TPM3": "TPM3" }, { "TPM3uf": "TPM3uf" }, { "TIM1": "TIM1" }, { "TIM1uf": "TIM1uf" }, { "TIM2": "TIM2" }, { "TIM2uf": "TIM2uf" }, { "TIM3": "TIM3" }, { "TIM3uf": "TIM3uf" }, { "TVMef": "TVMef" }, { "TVM": "TVM" }, { "SYM": "SYM" }, { "GTR": "GTR" } ], "value": "NA", "label": "Model name" }, { "name": "raxml_ng_gamma", "prefix": "+G", "type": "numeric", "value": 0, "min": 0, "max": "NA", "step": 1, "label": "Gamma for model parameter (+G{n})" }, { "name": "raxml_ng_spr_radius", "prefix": "--spr-radius", "type": "text", "value": "", "label": "SPR re-insertion radius for fast iterations (auto if empty)" }, { "name": "raxml_ng_spr_cutoff", "prefix": "--spr-cutoff", "type": "text", "value": "1.0", "label": "relative LH cutoff for descending into subtrees ('off' to deactivate)" } ] } ], "install": [], "citations": { "raxml_ng": [ "Alexey M Kozlov, Diego Darriba, Tom\u00e1\u0161 Flouri, Benoit Morel, Alexandros Stamatakis, RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference, Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4453-4455, https:\/\/doi.org\/10.1093\/bioinformatics\/btz305" ] }, "yaml": "{\n id: raxml_ng,\n name: RAxML-NG,\n article: \"10.1093\/bioinformatics\/btz305\",\n website: \"https:\/\/github.com\/amkozlov\/raxml-ng\",\n git: \"https:\/\/github.com\/amkozlov\/raxml-ng\",\n description: \"RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion\",\n version: \"1.2.0\",\n documentation: \"https:\/\/github.com\/amkozlov\/raxml-ng\/wiki\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: \"raxml_ng\",\n cname: \"raxml_ng\",\n command: \"raxml-ng\",\n category: \"phylogenetics\",\n output_dir: \"raxml_ng\",\n inputs: [\n { name: aligned_seqs, type: [\"aligned_fasta\", \"phylip\"], description: \"Aligned sequences\" , from: \"parameter\" },\n ],\n outputs:\n [\n { name: \"best_tree\", type: \"newick\", file: \"run.raxml.bestTree\", description: \"Best-scoring ML tree (strictly bifurcating)\" },\n { name: \"log\", type: \"txt\", file: \"run.raxml.log\", description: \"RAxML-NG log\" },\n ],\n options:\n [\n {\n name: raxml_ng_threads,\n prefix: \"--threads\",\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: raxml_ng_seed,\n prefix: \"--seed\",\n type: numeric,\n value: 1234,\n min: 0,\n max: NA,\n step: 1,\n label: \"seed for pseudo-random number generator\",\n },\n {\n name: raxml_ng_aligned_seqs,\n type: input_file,\n value: \"\",\n label: \"Path to aligned sequences file\",\n },\n {\n name: \"raxml_ng_model_name\",\n prefix: \"--model\",\n type: \"select\",\n choices:\n [\n JC: \"JC\",\n K80: \"K80\",\n F81: \"F81\",\n HKY: \"HKY\",\n TN93ef: \"TN93ef\",\n TN93: \"TN93\",\n K81: \"K81\",\n K81uf: \"K81uf\",\n TPM2: \"TPM2\",\n TPM2uf: \"TPM2uf\",\n TPM3: \"TPM3\",\n TPM3uf: \"TPM3uf\",\n TIM1: \"TIM1\",\n TIM1uf: \"TIM1uf\",\n TIM2: \"TIM2\",\n TIM2uf: \"TIM2uf\",\n TIM3: \"TIM3\",\n TIM3uf: \"TIM3uf\",\n TVMef: \"TVMef\",\n TVM: \"TVM\",\n SYM: \"SYM\",\n GTR: \"GTR\",\n ],\n value: \"NA\",\n label: \"Model name\",\n },\n {\n name: raxml_ng_gamma,\n prefix: \"+G\",\n type: numeric,\n value: 0,\n min: 0,\n max: NA,\n step: 1,\n label: \"Gamma for model parameter (+G{n})\",\n },\n {\n name: raxml_ng_spr_radius,\n prefix: \"--spr-radius\",\n type: text,\n value: \"\",\n label: \"SPR re-insertion radius for fast iterations (auto if empty)\",\n },\n {\n name: raxml_ng_spr_cutoff,\n prefix: \"--spr-cutoff\",\n type: text,\n value: \"1.0\",\n label: \"relative LH cutoff for descending into subtrees ('off' to deactivate)\",\n },\n ],\n },\n ],\n install: {\n # raxml_ng: [\n # \"cd \/opt\/biotools\/\",\n # \"mkdir raxml_ng && cd raxml_ng\",\n # \"wget https:\/\/github.com\/amkozlov\/raxml-ng\/releases\/download\/1.0.1\/raxml-ng_v1.0.1_linux_x86_64.zip\",\n # \"unzip raxml-ng_v1.0.1_linux_x86_64.zip\",\n # \"mv raxml-ng \/opt\/biotools\/bin\/\",\n # \"cd .. && rm -r raxml_ng\"\n # ],\n },\n citations: {\n raxml_ng: [\n \"Alexey M Kozlov, Diego Darriba, Tom\u00e1\u0161 Flouri, Benoit Morel, Alexandros Stamatakis, RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference, Bioinformatics, Volume 35, Issue 21, 1 November 2019, Pages 4453-4455, https:\/\/doi.org\/10.1093\/bioinformatics\/btz305\"\n ]\n }\n}\n" } ]