[ { "id": "mafft", "name": "MAFFT", "article": "10.1093\/molbev\/mst010", "website": "https:\/\/mafft.cbrc.jp\/alignment\/software\/", "git": "https:\/\/github.com\/GSLBiotech\/mafft", "description": "MAFFT: a multiple sequence alignment program", "version": "7.520", "documentation": "https:\/\/mafft.cbrc.jp\/alignment\/software\/manual\/manual.html", "multiqc": "custom", "commands": [ { "name": "mafft", "cname": "MAFFT", "command": "mafft", "category": "phylogenetics", "output_dir": "mafft", "inputs": [ { "name": "fasta", "type": "fasta_file", "file": "*.fasta", "description": "fasta file" } ], "outputs": [ { "name": "aligned_fasta", "type": "aligned_fasta", "file": "output.afa", "description": "aligned fasta file" } ], "options": [ { "name": "mafft_threads", "prefix": "--thread", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "mafft_fasta", "type": "input_file", "value": "", "label": "Path to fasta file" }, { "name": "mafft_matrix", "prefix": "", "type": "select", "choices": [ { "none": "none" }, { "BLOSUM 30": "--bl 30" }, { "BLOSUM 45": "--bl 45" }, { "BLOSUM 62": "--bl 62" }, { "BLOSUM 80": "--bl 80" }, { "JTT PAM 100": "--jtt 100" }, { "JTT PAM 200": "--jtt 200" } ], "value": "none", "label": "Matrix (protein only)" }, { "name": "mafft_gap_open", "prefix": "--op", "type": "numeric", "value": 1.53, "min": "NA", "max": "NA", "step": "NA", "label": "Gap opening penalty at group-to-group alignment" }, { "name": "mafft_gap_extension", "prefix": "--ep", "type": "numeric", "value": 0.123, "min": "NA", "max": "NA", "step": "NA", "label": "Offset value, which works like gap extension penalty, for group-to-group alignment" }, { "name": "mafft_order", "prefix": "", "type": "select", "choices": [ { "input order": "--inputorder" }, { "aligned order": "--reorder" } ], "value": "--inputorder", "label": "Output order" }, { "name": "mafft_retree", "prefix": "--retree", "type": "numeric", "value": 2, "min": "NA", "max": "NA", "step": 1, "label": "Guide tree is built times in the progressive stage. Valid with 6mer distance" }, { "name": "mafft_treeout", "prefix": "--treeout", "type": "checkbox", "value": false, "label": "Guide tree is output to the input.tree file" }, { "name": "mafft_maxiterate", "prefix": "--maxiterate", "type": "numeric", "value": 0, "min": "NA", "max": "NA", "step": 1, "label": " cycles of iterative refinement are performed" }, { "name": "mafft_ffts", "prefix": "", "type": "select", "choices": [ { "": "" }, { "localpair": "--localpair" }, { "genafpair": "--genafpair" }, { "globalpair": "--globalpair" } ], "value": "", "label": "Perform fast fourier transform" } ] } ], "install": [], "citations": { "mafft": [ "Kazutaka Katoh, Daron M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, Volume 30, Issue 4, April 2013, Pages 772-780, https:\/\/doi.org\/10.1093\/molbev\/mst010" ] }, "yaml": "{\n id: mafft,\n name: MAFFT ,\n article: \"10.1093\/molbev\/mst010\",\n website: \"https:\/\/mafft.cbrc.jp\/alignment\/software\/\",\n git: \"https:\/\/github.com\/GSLBiotech\/mafft\",\n description: \"MAFFT: a multiple sequence alignment program\",\n version: \"7.520\",\n documentation: \"https:\/\/mafft.cbrc.jp\/alignment\/software\/manual\/manual.html\",\n multiqc: \"custom\",\n commands:\n [\n {\n name: mafft,\n cname: \"MAFFT\",\n command: \"mafft\",\n category: \"phylogenetics\",\n output_dir: mafft,\n inputs: [{ name: fasta, type: \"fasta_file\", file: \"*.fasta\", description: \"fasta file\"}],\n outputs: [{ name: aligned_fasta, type: \"aligned_fasta\", file: \"output.afa\", description: \"aligned fasta file\"}],\n options: [\n {\n name: mafft_threads,\n prefix: --thread,\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: mafft_fasta,\n type: input_file,\n value: \"\",\n label: \"Path to fasta file\",\n },\n {\n name: \"mafft_matrix\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n none: \"none\",\n BLOSUM 30: \"--bl 30\",\n BLOSUM 45: \"--bl 45\",\n BLOSUM 62: \"--bl 62\",\n BLOSUM 80: \"--bl 80\",\n JTT PAM 100: \"--jtt 100\",\n JTT PAM 200: \"--jtt 200\",\n ],\n value: \"none\",\n label: \"Matrix (protein only)\",\n },\n {\n name: mafft_gap_open,\n prefix: --op,\n type: numeric,\n value: 1.53,\n min: NA,\n max: NA,\n step: NA,\n label: \"Gap opening penalty at group-to-group alignment\",\n },\n {\n name: mafft_gap_extension,\n prefix: --ep,\n type: numeric,\n value: 0.123,\n min: NA,\n max: NA,\n step: NA,\n label: \"Offset value, which works like gap extension penalty, for group-to-group alignment\",\n },\n {\n name: \"mafft_order\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n input order: \"--inputorder\",\n aligned order: \"--reorder\",\n ],\n value: \"--inputorder\",\n label: \"Output order\",\n },\n {\n name: mafft_retree,\n prefix: --retree,\n type: numeric,\n value: 2,\n min: NA,\n max: NA,\n step: 1,\n label: \"Guide tree is built times in the progressive stage. Valid with 6mer distance\",\n },\n {\n name: mafft_treeout,\n prefix: --treeout,\n type: checkbox,\n value: FALSE,\n label: \"Guide tree is output to the input.tree file\",\n },\n {\n name: mafft_maxiterate,\n prefix: --maxiterate,\n type: numeric,\n value: 0,\n min: NA,\n max: NA,\n step: 1,\n label: \" cycles of iterative refinement are performed\",\n },\n {\n name: \"mafft_ffts\",\n prefix: \"\",\n type: \"select\",\n choices:\n [\n no: \"\",\n localpair: \"--localpair\",\n genafpair: \"--genafpair\",\n globalpair: \"--globalpair\",\n ],\n value: \"\",\n label: \"Perform fast fourier transform\",\n },\n ],\n },\n ],\n install:\n {\n # mafft: [\n # \"cd \/opt\/biotools\/\",\n # \"wget https:\/\/mafft.cbrc.jp\/alignment\/software\/mafft_7.471-1_amd64.deb\",\n # \"dpkg -i mafft_7.471-1_amd64.deb\",\n # \"rm mafft_7.471-1_amd64.deb\"\n # ]\n },\n citations:\n {\n mafft: [\n \"Kazutaka Katoh, Daron M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, Volume 30, Issue 4, April 2013, Pages 772-780, https:\/\/doi.org\/10.1093\/molbev\/mst010\"\n ]\n },\n}\n" } ]