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MGR specifications

Information


Unique identifier OMICS_21807
Name MGR
Alternative names Multiple Genome Rearrangements, webMGR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A phylogenic tree and a representation.
Output format Newick,ASCII
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.01
Stability No
Source code URL http://grimm.ucsd.edu/DIST/MGR-2.01.tar.gz
Maintained No

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Information


Unique identifier OMICS_21807
Name MGR
Alternative names Multiple Genome Rearrangements, webMGR
Interface Web user interface
Restrictions to use None
Input data A uni- or multi-chromosomal genome.
Output data A representation of the unrooted tree recovered with clickable edges to display the possible optimal rearrangement events via the GRIMM web server, a pairwise distance matrix of the input genome and offers clickable pairwise scenarios and a signed permutation of the input genome as well as the ancestors recovered.
Output format ASCII
Computer skills Basic
Stability No
Maintained No

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Publications for Multiple Genome Rearrangements

MGR citations

 (44)
call_split

Partial arm translocations in evolution of malaria mosquitoes revealed by high coverage physical mapping of the Anopheles atroparvus genome

2018
BMC Genomics
PMCID: 5914054
PMID: 29688842
DOI: 10.1186/s12864-018-4663-4
call_split See protocol

[…] mum block size and gap threshold (a maximum distance between genes in a synteny block). Synteny blocks obtained by GRIMM-Synteny were visualized using genoPlotR []. The Multiple Genome Rearrangement (MGR) program [] was used to determine the number and types of rearrangements that caused the synteny block reshuffling among three species. To run the random model for synteny blocks, we obtained the […]

library_books

Ancestral Genome Reconstruction on Whole Genome Level

2017
Curr Genomics
PMCID: 5635614
PMID: 29081686
DOI: 10.2174/1389202918666170307120943

[…] es to track back the rearrangement events based on a parsimony assumption []. This algorithm was tested on simulated datasets and showed to have comparable sensitivity and higher specificity than the MGR algorithm []. EMRAE also processed same mammalian genome data that used in InferCARs [], and predicted 1109 rearrangement events including 831 inversions, 15 translocations, 237 transpositions, an […]

library_books

Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae

2017
Sci Rep
PMCID: 5430533
PMID: 28428552
DOI: 10.1038/s41598-017-01144-1

[…] ix of 98 genes from 15 ulvophycean chloroplast genomes. The branch lengths of this tree were computed on the tree topology inferred from the RAxML analyses of the sequence data using the -t option of MGR v2.03. Because MGR cannot handle duplicated genes, only one copy of the IR and of each duplicated gene was included in the matrix. […]

library_books

The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

2017
PeerJ
PMCID: 5399880
PMID: 28439458
DOI: 10.7717/peerj.3162

[…] iqhucha str. N139 in comparison to other Exiguobacterium species, nucleotide syntenic blocks were obtained with Mauve version 2.3.1 (). Syntenic block permutations were exported and used as input for MGR (). MGR was used to calculate the minimum number of rearrangements between the species analyzed, and to recover the rearrangement dendrogram. genoPlotR () was used to plot the syntenic blocks ().T […]

library_books

Genus Wide Screening Reveals Four Distinct Types of Structural Plastid Genome Organization in Pelargonium (Geraniaceae)

2016
Genome Biol Evol
PMCID: 5381562
PMID: 28172771
DOI: 10.1093/gbe/evw271

[…] hes. Partial sequences (psbZ–trnSUGA spacer, trnSGGA–rps4) of Geranium palmatum, E . carvifolium, and Monsonia speciosa (; ) were used as outgroup.The plastome rearrangement history was analyzed with MGR () under a linear and undirected model over the fixed ML topology. We first restricted this reconstruction to our PCR-screened regions, that is, psbZ, trnSGGA, rps4, rbcL, psaI, rps18, rpl20, ndhF […]

library_books

Fast ancestral gene order reconstruction of genomes with unequal gene content

2016
BMC Bioinformatics
PMCID: 5123410
PMID: 28185578
DOI: 10.1186/s12859-016-1261-9

[…] alysis [], the first proposed method, which was based the breakpoint distance, many other distance-based methods were developed, with different distances, such as the reversal distance (GRAPPA [] and MGR []), the double cut and join (DCJ) distance [, ] (PATHGROUPS [], GASTS [] and MGRA [, ]), and the single cut or join (SCJ) distance [] (SCJ Small Phylogeny []), just to cite a few examples.Another […]

Citations

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MGR institution(s)
Department of Mathematics, University of Southern California, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
MGR funding source(s)
Supported by grants from the National Sciences and Engineering Research Council of Canada.

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