MUSCLE is an application for aligning biological sequences and protein structures. Multiple sequence alignment is a fundamental task in molecular biology, helping researchers identify conserved regions, investigate evolutionary relationships and compare the functional characteristics of related sequences.
The software processes collections of nucleotide or amino acid sequences and determines corresponding positions that are likely to represent shared evolutionary ancestry. Its alignment algorithms are designed to provide high accuracy while accommodating datasets containing large numbers of sequences.
MUSCLE also supports ensembles of alternative alignments. These allow researchers to examine how uncertainty in sequence alignment can influence subsequent analyses, including phylogenetic tree reconstruction and predictions of biological structure. Protein structure alignment extends its functionality beyond traditional sequence comparison.
This is free and open source software.
Key Features
- Multiple sequence alignment of nucleotide and amino acid datasets.
- High-accuracy alignment algorithms designed for datasets ranging from small collections to thousands of sequences.
- Generation of alternative alignment replicates to investigate uncertainty in homology assignments.
- Ensemble-based analysis that enables researchers to compare results obtained from different plausible alignments.
- Protein structure alignment using structural information prepared with the associated Reseek tools.
- Support for large protein structure collections through distance-matrix-assisted alignment workflows.
- Configurable alignment procedures for balancing computational cost and alignment accuracy.
- FASTA-based input and output suitable for integration with other bioinformatics applications.
- Command-line interface for reproducible analysis and automated processing of sequence collections.
- Facilities for examining alignment variability and its potential influence on downstream biological interpretation.
- Suitable for comparative genomics, phylogenetics, protein analysis and other molecular biology research.
Website: www.drive5.com/muscle
Support:
Developer: Robert C. Edgar
License: GNU General Public License v3.0
MUSCLE is written in C++. Learn C++ with our recommended free books and free tutorials.
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