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MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.This tool can align up to 500 sequences or a maximum file size of 1 MB.
MUSCLE is widely-used software for making multiple alignments of biological sequences. Version 5 of MUSCLE achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences on a commodity desktop computer.
Aug 19, 2004 · Multiple Sequence Alignment Program. In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks.
Mar 1, 2004 · The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets.
Sep 1, 2004 · We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog).
MUltiple Sequence Comparison by Log-Expectation ( MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004.
pacagek muscle integrates the MUSCLE algorithm into the Bioconductor project by utilizing existing Biostrings classes for representing sequence objects and multiple alignments. Contents
Nov 12, 2021 · Muscle v5 is a major re-write of MUSCLE based on new algorithms. Highest accuracy, scalable to thousands of sequences. Compared to previous versions, Muscle v5 is much more accurate, is often faster, and scales to much larger datasets.
Aug 19, 2004 · We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three ...
muscle. Multiple Sequence Alignment with MUSCLE. DOI: 10.18129/B9.bioc.muscle. Bioconductor version: Release (3.19) MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. Author: Algorithm by Robert C. Edgar. R port by Alex T. Kalinka. Maintainer: Alex T. Kalinka <alex.t.kalinka at gmail.com>
