Mugsy protocols

Mugsy specifications


Unique identifier OMICS_03606
Name Mugsy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 1.2.3
Stability Stable
Maintained Yes



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  • person_outline Samuel V. Angiuoli <>

Publication for Mugsy

Mugsy IN pipelines

PMCID: 5891936
PMID: 29643938
DOI: 10.1186/s13099-018-0242-0

[…] lead to mis-assembly. the lack of collinearity between the reference genome and these new assemblies also impaired the ability to align them for base-level comparisons. alignment programs like mugsy and mauve [15] allow artificial re-arrangements of sequences to create locally collinear blocks (lcbs) for alignment. in our reference-guided approach, we added a manual curation step […]

PMCID: 5742254
PMID: 29312366
DOI: 10.3389/fpls.2017.02064

[…] the methodology depicted by yang et al. (2014). briefly, the fasta files for a and b subgenomes were downloaded from peanutbase site ( and indels were identified using mugsy software (angiuoli and salzberg, 2011). the alignment results were mined for indel polymorphism using the perl scripts provided by dr. wencai yang (china agricultural university, beijing, […]

PMCID: 4835932
PMID: 27096008
DOI: 10.1186/s13099-016-0096-2

[…] of nccp15738 were searched using the phast server [24] (data not shown)., to infer the evolutionary history of nccp15738, we performed a multiple sequence alignment of the whole genome using mugsy (version 1.2.3) [25] and approximately-maximum-likelihood phylogenetic trees were inferred using fasttree (version 2.1.7) [26] with a gtr (generalized time-reversible) + cat model [27]. […]

PMCID: 5036109
PMID: 27688977
DOI: 10.7717/peerj.2484

[…] from each group as defined in the database) ( and the 13 local sputum strains., this was followed by pairwise-alignment and comparisons using mugsy (angiuoli & salzberg, 2011), with default parameters, to identify the positions of rearranged regions in um-csf strains., for this analysis, we downloaded from ncbi’s sra database, […]

PMCID: 4415261
PMID: 25932050
DOI: 10.1186/s13099-015-0059-z

[…] tw10722 (nz_aelb01000001.1), and tw10828 (nz_aelc01000001.1) were downloaded from the ncbi website (table 1). multiple sequence alignments of escherichia coli genomes were performed with mugsy [18]. the trees were constructed based on core snps (single nucleotide polymorphisms) from whole genome alignment by using the maximum-likelihood method in phylogeny inference package […]

Mugsy institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

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