MUSCLE protocols

MUSCLE specifications

Information


Unique identifier OMICS_00982
Name MUSCLE
Alternative name MUltiple Sequence Comparison by Log- Expectation
Interface Web user interface
Restrictions to use None
Input data PEARSON, FASTA, ClustalW, HTML, GCG MSF, PHYLIP
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Robert Edgar <>
  • person_outline Rodrigo Lopez <>

Additional information


https://www.drive5.com/muscle/manual/

Information


Unique identifier OMICS_00982
Name MUSCLE
Alternative name MUltiple Sequence Comparison by Log- Expectation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Version 3.8.31
Stability Stable
Source code URL https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
Maintained Yes

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Versioning


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Maintainers


  • person_outline Robert Edgar <>
  • person_outline Rodrigo Lopez <>

Additional information


https://www.drive5.com/muscle/manual/

Publications for MUltiple Sequence Comparison by Log- Expectation

MUSCLE IN pipelines

 (587)
2018
PMCID: 5752868
PMID: 29101189
DOI: 10.1128/AEM.01712-17

[…] strain sequences in the genbank database (https://www.ncbi.nlm.nih.gov/genbank/) using the blastn program. each isolate sequence was aligned with type reference strain (genbank database) using muscle (79). phylogenetic trees were generated from the aligned sequences using the mega 6 software program (80), which calculates evolutionary distances using the kimura 2-parameter model (81). […]

2018
PMCID: 5761093
PMID: 29316927
DOI: 10.1186/s12936-017-2157-5

[…] databases. sixty-one ldh sequences were included in the phylogenetic tree reconstruction (additional files 2, 3). the best-fit substitution model for the multiple sequence alignment generated by muscle was determined using the bayesian information criteria (bic) strategy in jmodeltest [38]. evolutionary relationships of the aligned sequences were determined using neighbour-joining (nj) […]

2018
PMCID: 5762703
PMID: 29321589
DOI: 10.1038/s41598-017-18695-y

[…] the minimum length of the regions is 6 amino acids and that they are formed by a single amino acid., for each of the two ortholog categories (with and without outgroup) we obtained alignments with muscle using default values57. because repetitive regions, such as hprs, are known to be difficult to align, all further hprs-related analyses (i.e., conservation, functional, and ancestral state […]

2018
PMCID: 5762865
PMID: 29321538
DOI: 10.1038/s41598-017-18791-z

[…] vaccine selection meeting for each season individually and calculated the genealogy and sd plots., we generated multiple sequence alignments from both the nucleotide or amino acid sequences with muscle66. to avoid shifts in the numbering of both alignments, positions with gaps in more than 80% of the sequences are removed from the alignment with trimal67. a phylogenetic tree was inferred […]

2018
PMCID: 5769438
PMID: 29335005
DOI: 10.1186/s40168-017-0387-y

[…] were combined within a non-redundant set. proteins were clustered in protein families by homology, using cd-hit with parameters of 80% identity and 80% coverage. each protein family was aligned by muscle v. 3.7 [31] with default parameters and a hidden markov model (hmm) was built for each family with hmmbuild function of the hmmer3 [32] using default parameters. hmmer search function […]

MUSCLE institution(s)
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA

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