GRAPPA specifications

Information


Unique identifier OMICS_22751
Name GRAPPA
Alternative names Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms, SA_GRAPPA, GRAPPA-2.0
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Bernard Moret <>
  • person_outline Jijun Tang <>

Publications for Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

GRAPPA in publications

 (11)
PMCID: 5408090
PMID: 28431152
DOI: 10.1093/gbe/evx071

[…] the default parameters. before the alignment, the stop codon of psba was specified as the starting point for all compared plastomes. on the basis of the yielded matrix of lcbs (, online), we used grappa v2.0 (; ) with the default parameters to estimate the pairwise breakpoint distance (the number of nonconserved adjacencies between genomes) as well as the pairwise inversion distance (the […]

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

[…] since bpanalysis [], 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 […]

PMCID: 3814193
PMID: 24022472
DOI: 10.1093/gbe/evt135

[…] to maximum parsimony (mp) analysis using paup 4.0b10 (). confidence of branch points was estimated by 1,000 bootstrap replications., phylogenies based on inversion medians were inferred with grappa 2.0 (http://www.cs.unm.edu/∼moret/grappa/, last accessed september 27, 2013) using the algorithm of and a data set of 55 gene/pseudogene positions. although this software can use breakpoint […]

PMCID: 3394415
PMID: 22369143
DOI: 10.1186/1471-2164-13-S1-S7

[…] orders of ancestral genomes has the potential to provide detailed information about the recent evolution of species descended from them. current popular tools to infer ancestral genome data (such as grappa and mgr) are all parsimony-based direct optimization methods with the aim to minimize the number of evolutionary events. recently a new method based on the approach of maximum likelihood […]

PMCID: 2858039
PMID: 20370914
DOI: 10.1186/1471-2105-11-168

[…] widely used methods to reconstruct phylogenies from gene order data, including distance-based methods (neighbor-joining [] and fastme []), bayesian (badger []) and direct optimization methods (grappa [] and mgr []). using corrected inversion distances, wang et al. showed that high-quality phylogenies can be obtained using distance-based methods such as neighbor-joining and fastme []. […]


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GRAPPA institution(s)
Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, USA; Department of Computer Science, University of New Mexico, Albuquerque, NM, USA
GRAPPA funding source(s)
Supported, in part, by NSF grants CAREER 00-93039, ITR 00-81404, and DEB 99- 10123; and by DOE CSRI 14968 and, in part, by NSF grant ITR 00-81404 and by the UNM Albuquerque High Performance Computing Center.

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