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Jul 20, 2023
MUltiple Sequence Comparison by Log-Expectation
MUSCLE is multiple alignment software for protein and nucleotide sequences. The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options.
Edgar, R. C. 2004 MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 325 1792-1797.
Edgar, R. C. 2004 MUSCLE a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 51 113.
The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper.
Checkout these related ports:
- Wise - Intelligent algorithms for DNA searches
- Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
- Vt - Discovers short variants from Next Generation Sequencing data
- Vsearch - Versatile open-source tool for metagenomics
- Viennarna - Alignment tools for the structural analysis of RNA
- Velvet - Sequence assembler for very short reads
- Vcftools - Tools for working with VCF genomics files
- Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
- Vcf2hap - Generate .hap file from VCF for haplohseq
- Vcf-split - Split a multi-sample VCF into single-sample VCFs
- Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
- Unanimity - Pacific Biosciences consensus library and applications
- Ugene - Integrated bioinformatics toolkit
- Ucsc-userapps - Command line tools from the UCSC Genome Browser project
- Trimmomatic - Flexible read trimming tool for Illumina NGS data