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The MUSCLE algorithm is for gene level alignment of either protein or nucleotide sequences. To run a MUSCLE alignment, select two or more sequences and Before use, read through this User's Guide to ensure proper use. User's Guide, please read “CM2 User's Guide” for installation or operation of Cool Muscle.MUSCLE User Guide. Multiple sequence comparison by log-expectation. by Robert C. Edgar. Version 3.5. August 2004. /muscle. email: muscle (at) drive5.com. MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE is The default settings will fulfill the needs of most users.More options. 9 Apr 2014 Task Name: align. Performs multiple sequence alignment with MUSCLE algorithm and saves the resulting alignment to file. Source data can be Complete Documentation of the Cool Muscle. Cool Muscle Brochure CM2 (Rev C) User Guide - Programming CML, pdf, 1.54 MB, May 01, 2014, CM2 (Rev 4 Feb 2014 Unipro UGENE Online User Manual v. To use this feature select the Align ? Align sequences to profile with MUSCLE context menu item. A fundamental step in the MUSCLE algorithm is aligning two multiple sequence alignments. This operation is sometimes called "profile-profile alignment". MUSCLE User Guide. Multiple sequence comparison by log-expectation. by Robert C. Edgar. Version 3.8. May 2010. /muscle · robert@drive5.com. Citation:.