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Protocols

GRAPPA specifications

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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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  • person_outline Bernard Moret
  • person_outline Jijun Tang

Publications for Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms

GRAPPA citations

 (14)
library_books

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

2017
Genome Biol Evol
PMCID: 5408090
PMID: 28431152
DOI: 10.1093/gbe/evx071

[…] th 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 minim […]

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

[…] ee. 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 a few ex […]

call_split

Phylo SI: a new genome wide approach for prokaryotic phylogeny

2013
Nucleic Acids Res
PMCID: 3936750
PMID: 24243847
DOI: 10.1093/nar/gkt1138
call_split See protocol

[…] The following reconstruction methods we compared in this study. We used the Phylo SI method described above with k = 10 based on the simulation results and biological rational. The GRAPPA toolbox for inversion/breakpoints distance-based phylogenetic reconstruction was taken from ().We also implemented two additional whole-genome–based methods to compare with the former two: Dire […]

call_split

Tracing the Evolution of Streptophyte Algae and Their Mitochondrial Genome

2013
Genome Biol Evol
PMCID: 3814193
PMID: 24022472
DOI: 10.1093/gbe/evt135
call_split See protocol

[…] subjected 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 me […]

library_books

A mixture framework for inferring ancestral gene orders

2012
BMC Genomics
PMCID: 3394415
PMID: 22369143
DOI: 10.1186/1471-2164-13-S1-S7

[…] n calculation, which is to optimize each ancestral node in terms of its three or more immediate neighbors, the phylogeny and ancestral genomes could be reconstructed. Current popular methods (such as GRAPPA [], MGR [] and their new improved versions) all use this approach and can infer ancestral gene orders with high accuracy. However these methods are extremely slow especially when the rearrangem […]

library_books

Rec DCM Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time

2011
PLoS One
PMCID: 3160844
PMID: 21887219
DOI: 10.1371/journal.pone.0022483

[…] acy of COGNAC as a consequence, and this section provides two examples to illustrate this. depicts a model tree used to generate test data and two reconstructed trees using an original MP method (the GRAPPA method) and COGNAC . For the result, the length of an edge is identical to the inversion distance between the two genomes in each side of the edge–this is smaller than the number of inversions […]


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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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