{"added":null,"apiVersion":1,"behindSince":"2026-07-21","buildDepends":[],"categories":["biology"],"comment":"MUltiple Sequence Comparison by Log-Expectation","compare":"/compare/muscle/index.json","dependentCount":null,"description":"MUSCLE is multiple alignment software for protein and nucleotide sequences.\nThe name stands for multiple sequence comparison by log-expectation.\n\nA range of options is provided that give you the choice of optimizing\naccuracy, speed, or some compromise between the two. Default parameters are\nthose that give the best average accuracy in the published tests. MUSCLE\ncan achieve both better average accuracy and better speed than CLUSTALW or\nT-Coffee, depending on the chosen options.\n\nCitation:\n\nEdgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy\nand high throughput. Nucleic Acids Research 32(5): 1792-1797.\n\nEdgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with\nreduced time and space complexity. BMC Bioinformatics 5(1): 113.\n\nThe NAR paper gives only a brief overview of the algorithm and\nimplementation details. For a full discussion of the method and many of\nthe non-default options that it offers, please see the BMC paper.","flavors":[],"html":"https://daemonports.org/dragonfly/biology/muscle/","kind":"port","lastUpdate":null,"license":["PD"],"maintainer":"mzaki@e-mail.ne.jp","name":"muscle","newest":false,"newestVersion":"5.1","noVulnData":false,"origin":"biology/muscle","otherSystems":[{"maintainer":"mzaki@e-mail.ne.jp","newest":true,"origin":"biology/muscle","path":"/biology/muscle/","system":"FreeBSD","updated":"2026-09-11","version":"5.1_1"},{"behindSince":"2026-07-21","maintainer":"bacon@NetBSD.org","matchedBy":"name","origin":"wip/muscle","path":"/netbsd/wip/muscle/","system":"NetBSD","version":"3.8.31"},{"maintainer":"mzaki@e-mail.ne.jp","newest":true,"noVulnData":true,"origin":"biology/muscle","path":"","system":"HardenedBSD","version":"5.1_1"},{"maintainer":"mzaki@e-mail.ne.jp","newest":true,"noVulnData":true,"origin":"biology/muscle","path":"","system":"GhostBSD","version":"5.1_1"}],"packages":null,"pkgName":"muscle-3.8.1551","related":null,"repository":"DPorts","requiredBy":[],"requiredByCount":0,"runDepends":[],"status":null,"system":"dragonfly","systemLabel":"DragonFly","version":"3.8.1551","versions":null,"vulnerabilities":null,"www":"https://www.drive5.com/muscle/"}