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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> <html lang="en"> <head> <meta http-equiv="Content-Language" content="en-us"> <meta http-equiv="Content-Type" content="text/html; charset=windows-1252"> <meta http-equiv="Content-Style-Type" content="text/css"> <meta http-equiv="Cache-Control" content="no-cache, no-store, must-revalidate"> <meta http-equiv="Pragma" content="no-cache"> <meta http-equiv="Expires" content="0"> <title>MUSCLE</title> <style type="text/css"> .Text { font-family:Arial; font-size:10pt; color:black; text-align:left; line-height:100%;} .ManText120 { font-family:Arial; font-size:10pt; color:black; text-align:left; line-height:120%; } </style> <link rel="stylesheet" type="text/css" href="https://drive5.com/styles.css"> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-50117757-1', 'drive5.com'); ga('send', 'pageview'); </script> </head> <body style="background-color:#c0c0c0;"> <div style="position:absolute; top:10px; left:20px; width:850px; height:60px;" > <span class="NavButtonPara"><a class="NavButton" href="/">Home</a></span> <span class="NavButtonPara"><a class="NavButton" href="/software.html">Software</a></span> <span class="NavButtonPara"><a class="NavButton" href="/services.html">Services</a></span> <span class="NavButtonPara"><a class="NavButton" href="/about.html">About</a></span> <span class="NavButtonPara"><a class="NavButton" href="/contact.html">Contact</a></span> </div> <div style="position:absolute; top:40px; left:20px; width:850px; height:100px;" > <img alt="Muscle v5" src="https://drive5.com/images/muscle5_banner.jpg"> </div> <div style="position:absolute; top:115px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;"> <div id="sidebar" style="background-color:#ffffff; position:absolute; top:-85px; left:855px; width:200px; min-height:585px; height:auto; overflow:hidden; " class="Text" > <a href="https://twitter.com/intent/follow?original_referer=http%3A%2F%2Fwww.drive5.com%2Fusearch%2Fmanual%2F&ref_src=twsrc%5Etfw&region=follow_link&screen_name=RobertEdgarPhD&tw_p=followbutton"> <img alt="Follow on twitter" src="https://drive5.com/images/follow.gif"></a><br><br> <span class="timeline-Footer u-cf"> <a href="https://twitter.com/RobertEdgarPhD"> <img alt="Robert C. Edgar on twitter" src="https://drive5.com/images/rcetwitter2.jpg" height="46" width="177"></a><br> </span> <div style="position:relative; float:left; padding: 0px;"> <div class="ManText120" dir="ltr" lang="en"> <a href="https://drive5.com/newproj.html"> <img src="https://drive5.com/images/newproj.png"></a><br> <div style="padding:6px"> <br> <span style="font-weight:bold; background-color:yellow;">120,000 new RNA virus species discovered </span> by mining the SRA (<a href="https://www.biorxiv.org/content/10.1101/2020.08.07.241729v2">paper</a>).<br><br /> Syncmers are better than minimizers (<a href="https://peerj.com/articles/10805">paper</a>).<br><br /> 16S analysis <a href="https://drive5.com/usearch/manual/videos.html">Video talks</a>.<br> <br><a href="https://drive5.com/urmap/">URMAP</a> ultra-fast read mapper (<a href="https://www.biorxiv.org/content/10.1101/2020.01.12.903351v1">paper)</a>.<br> <br>~20% of taxonomy annotations in SILVA and Greengenes are wrong (<a href="https://peerj.com/articles/5030/">paper</a>).<br> <br>Taxonomy prediction is <50% accurate for 16S V4 sequences (<a href="https://peerj.com/articles/4652/">paper</a>).<br> <br>97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (<a href="https://doi.org/10.1101/192211">paper</a>).<br> </div></div><br> </div> </div> <div style="position:relative; float:left; top:0px; width:220px;"> <div class="YellowBackground"> <br> <span class="BlueExtraSmall">MUSCLE has been cited by</span><br> <span class="BlueLarge"> 58,408 papers </span><br> <span class="BlueExtraSmall"> <a href="http://scholar.google.com/citations?user=RzVMRc0AAAAJ&hl=en">Google scholar</a><br> Last updated 26 Feb 2025 <br> </span> </div> <div style="font-size:8pt;"> </div> <div class="ButtonPara"><a class="Button" href="https://github.com/rcedgar/muscle/releases/latest">Download</a></div> <div style="font-size:2pt;"> </div> <div class="ButtonPara"><a class="Button" href="https://drive5.com/muscle5/manual">Documentation</a></div> <div style="font-size:2pt;"> </div> <div class="ButtonPara"><a class="Button" href="https://drive5.com/muscle5/manual/support.html">Support and feedback</a></div> <div style="font-size:2pt;"> </div> <div class="ButtonPara"><a class="Button" href="https://drive5.com/muscle/downloads_v3.htm">MUSCLE v3</a></div> <div style="font-size:8pt;"> </div> <br> <br> </div> <div style="position:relative; float:left; top:0px; width:550px; left:25px;"> <span class="Head">Next-generation MUSCLE</span><br> <div class="ManText"> Muscle v5 is a major re-write of MUSCLE based on new algorithms. </div> <p class="ManText"> <span class="Head">Highest accuracy, scalable to thousands of sequences</span><br> Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets. At the time of writing (late 2021), Muscle v5 has the highest scores on multiple alignment benchmarks including Balibase, Bralibase, Prefab and Balifam. It can align tens of thousands of sequences with high accuracy on a low-cost commodity computer (say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5 is 20-30% more accurate than MAFFT and Clustal-Omega. </p> <a href="https://www.youtube.com/watch?v=2HmjHStpu7I"> <img src="https://drive5.com/muscle5/manual/youtube_talk_muscle5.png" style="float:right;"/></a> <p class="ManText"> <span class="Head">Alignment ensembles</span><br> Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on benchmark test, including the MSA made with default parameters. By comparing results of downstream analysis (trees, structure prediction...) on different replicates, you can assess the effects of alignment errors on your study. </p>  <br> </div> </div> </body> </html>