https://github.com/rcedgar/muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
https://github.com/rcedgar/muscle

algorithms bioinformatics biology nucleotide-alignment protein-alignment protein-structure protein-structure-alignment sequence-clustering sequence-search

Last synced: 1 day ago
JSON representation

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

• Host: GitHub
• URL: https://github.com/rcedgar/muscle
• Owner: rcedgar
• License: gpl-3.0
• Created: 2021-06-19T21:32:31.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-12-06T16:28:28.000Z (27 days ago)
• Last Synced: 2024-12-25T14:12:47.808Z (8 days ago)
• Topics: algorithms, bioinformatics, biology, nucleotide-alignment, protein-alignment, protein-structure, protein-structure-alignment, sequence-clustering, sequence-search
• Language: C++
• Homepage: https://drive5.com/muscle
• Size: 67.8 MB
• Stars: 223
• Watchers: 7
• Forks: 23
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

Awesome Lists containing this project

README

        
![Muscle5](http://drive5.com/images/muscle5_header.jpg)

Muscle is widely-used software for making multiple alignments of biological sequences. 

Muscle achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences or structures on a commodity desktop computer.

Muscle supports generating an ensemble of alternative alignments with the same high accuracy obtained with default parameters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment variation caused by ambiguities and errors.

### Multiple structure alignment

Structure alignment ("Muscle-3D") is supported as well as conventional amino acid sequence alignment. Input for structure alignment is a "mega" file generated by the `pdb2mega` command of `reseek` (https://github.com/rcedgar/reseek).

[](https://www.youtube.com/watch?v=BzIgqdm9xDs)


# for up to ~100 structures

reseek -pdb2mega STRUCTS -output structs.mega

muscle -align structs.mega -output structs.afa


# for up to ~10,000 structures

reseek -convert STRUCTS -bca structs.bca

reseek -pdb2mega structs.bca -output structs.mega

reseek -distmx structs.bca -output structs.distmx

muscle -super7 structs.mega -distmxin structs.distmx -reseek -output structs.afa



### Downloads and installation

Binary files are self-contained, no dependencies. To install, download the binary and make sure the execute bit is set.

https://github.com/rcedgar/muscle/releases

### Documentation

[Muscle v5 home page](https://drive5.com/muscle5)   

[Manual](https://drive5.com/muscle5/manual)   

### Building MUSCLE from source

[https://github.com/rcedgar/muscle/wiki/Building-MUSCLE](https://github.com/rcedgar/muscle/wiki/Building-MUSCLE)

### References

Edgar RC., Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. Nature Communications 13.1 (2022): 6968.    

[https://www.nature.com/articles/s41467-022-34630-w.pdf](https://www.nature.com/articles/s41467-022-34630-w.pdf)

Edgar RC. and Tolstoy I., Muscle-3D: scalable multiple protein structure alignment (2024) BioRxiv.