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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

Download


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Versioning


No version available

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 citations

 (7215)
call_split

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

2018
mSystems
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] ion (). 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 u […]

call_split

Smooth muscle like Ca2+ regulation of actin–myosin interaction in adult jellyfish striated muscle

2018
Sci Rep
PMCID: 5958069
PMID: 29773804
DOI: 10.1038/s41598-018-24817-x
call_split See protocol

[…] ranscript level, except for the sponge MHC-II isoforms, the amino acid sequences of which have been predicted from the genomic sequence by automated analysis. Multiple alignments were prepared by the MUSCLE algorithm in Genetyx-Win Ver. 13 (Genetyx) with default settings, and the results were used to construct neighbor-joining phylogenetic trees by using MEGA7 with bootstrap replication set at 100 […]

library_books

Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

2018
Sci Adv
PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] onplacental 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 Axel […]

library_books

Components of a new gene family of ferroxidases involved in virulence are functionally specialized in fungal dimorphism

2018
Sci Rep
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 by […]

library_books

Optical functionalization of human Class A orphan G protein coupled receptors

2018
Nat Commun
PMCID: 5956105
PMID: 29769519
DOI: 10.1038/s41467-018-04342-1

[…] 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 and as […]

library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] ralist entomopathogens (). The higher signal peptide number in O. unilateralis than in O. sinensis may contribute to a process described in a recent finding in which O. unilateralis cells invade host muscle fibers and form networks throughout the body to perform the manipulations (). Similar patterns have been revealed in the Harpellales (Zoopagomycota; Kickxellomycotina). The hosts of Smittium mu […]

Citations

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

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