MUSCLE protocols

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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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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

 (1031)
2018
PMCID: 5693036
PMID: 29061367
DOI: 10.1016/j.ygcen.2017.10.009

[…] than the highest predicted tertiary structure tm predicted by oligoanalyzer 3.1 online software (integrated dna technologies). chicken cck and gastrin preprohormone mrna sequences were aligned using muscle () to identify regions that were divergent and to avoid selecting regions of similarity between the two transcripts for targeting oligonucleotide primer and probe annealing (). similarity […]

2018
PMCID: 5749766
PMID: 29293601
DOI: 10.1371/journal.pone.0190266

[…] distances. the phylogeny of synechococcus was constructed using all identified 566 core proteins. multiple sequence alignment was conducted separately on proteins in each core cluster by using muscle []; all alignments in each strain were concatenated in the same order. subsequently, neighbor-joining trees were constructed using mega [] (ver. 7.0.14) with several options (100 […]

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 (). phylogenetic trees were generated from the aligned sequences using the mega 6 software program (), which calculates evolutionary distances using the kimura 2-parameter model (). […]

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 , ). the best-fit substitution model for the multiple sequence alignment generated by muscle was determined using the bayesian information criteria (bic) strategy in jmodeltest []. 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 values. 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 […]


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MUSCLE in publications

 (4070)
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] (). genes on the assembled contigs were predicted with prokka () using the settings --kingdom viruses and an e value of 1e−5. multiple alignments of genes and genomes were made in mega7 using the muscle algorithm with default settings (, ). the alignments were manually trimmed, and phylogenetic trees were built using the maximum-likelihood method in mega7 with the default settings. sequences […]

PMCID: 5958069
PMID: 29773804
DOI: 10.1038/s41598-018-24817-x

[…] tropomyosin, but not troponin, which is known to activate contraction dependent on intracellular ca2+ signaling in almost all striated muscles of bilaterians. notably, the myosin comprised striated muscle-type heavy chain and smooth muscle-type regulatory light chains. in the presence of ca2+, the mg-atpase activity of actomyosin was stimulated and ser21 of the regulatory light chain […]

PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] mammal vertebrate taxa and a chit1 (chitotriosidase) outgroup (nm_003465), imported all of the sequences into geneious, aligned them using multiple sequence comparison by log-expectation (muscle) (), manually adjusted the alignments, and removed sequences and sequence positions determined by eye to have dubious homology (data set s1). we then estimated a gene tree using randomized […]

PMCID: 5955967
PMID: 29769603
DOI: 10.1038/s41598-018-26051-x

[…] so the relative gene expression of the above mentioned genes could be obtained using the delta-delta ct (δδct) method normalizing for rrna 18s. multiple protein sequence alignment was conducted with muscle program, and then curated by gblocks to select conserved blocks of amino acids. computational phylogenetic analysis was performed using phyml software. phylogenetic relationship was inferred […]

PMCID: 5956105
PMID: 29769519
DOI: 10.1038/s41467-018-04342-1

[…] sequences of restriction enzymes used in the cloning steps were removed from the nucleotide sequences using macros written in igor pro (wavemetrics)., a multiple sequence alignment generated using muscle, and a series of macros written in igor pro were used to design the chimeric receptors. first, protein and nucleotide sequences (including those of rhodopsin) were imported into igor pro […]


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

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