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EEEP specifications

Information


Unique identifier OMICS_25367
Name EEEP
Alternative name Efficient Evaluation of Edit Paths
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL http://bioinformatics.org.au/tools/eeep/EEEP-1.01-source.tar.gz
Maintained Yes

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Versioning


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Maintainers


  • person_outline Robert Beiko
  • person_outline Nicholas Hamilton

Publication for Efficient Evaluation of Edit Paths

EEEP citations

 (11)
library_books

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

2017
Viruses
PMCID: 5408678
PMID: 28387730
DOI: 10.3390/v9040072

[…] often via statistical analysis like bipartitions, quartet bipartitions, etc. [,]; or (ii) by examining gene history, through phyletic profiles []. Several algorithms like LatTrans [], HorizStory [], Efficient Evaluation of Edit Paths [] and PhyloNet package including RIATA-HGT [] and T-REX [] are available to detect HGT events.Members of the proposed order Megavirales have been shown over the pas […]

library_books

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

2017
Mol Biol Evol
PMCID: 5455968
PMID: 28383641
DOI: 10.1093/molbev/msx111

[…] identifying a recombination event, RDP4 implements a hidden Markov model to estimate breakpoint positions. Then, RDP4 identifies the probable recombinant sequence using the PHYLPRO (), VISRD (), and EEEP () methods. Bonferrroni corrections were applied to set the family-wise error rate to 0.05. We tested the whole-plastome alignment for recombination and an alignment stripped of gaps and poorly a […]

call_split

Mitochondrial DNA Variation and Introgression in Siberian Taimen Hucho taimen

2013
PLoS One
PMCID: 3741329
PMID: 23951096
DOI: 10.1371/journal.pone.0071147
call_split See protocol

[…] ation using various recombination detection methods implemented in the program RDP3 . The parental and recombinant sequences were determined using the VisRD method , modified version of PHYLPRO , and EEEP also implemented in RDP3 (default settings). […]

call_split

New approaches for unravelling reassortment pathways

2013
BMC Evol Biol
PMCID: 3541980
PMID: 23279962
DOI: 10.1186/1471-2148-13-1
call_split See protocol

[…] ee topologies, Robinson-Foulds (RF) distances between the trees were calculated using PAUP. We then carried out 56 pairwise comparisons (all possible pairwise comparisons of the 8 segments) using the EEEP (Efficient Evaluation of Edit Paths) software []. EEEP is a program that seeks to reconcile a reference tree and a test tree, by finding the minimum number of SPR moves required to convert the fo […]

library_books

Phylogeny rather than ecology or lifestyle biases the construction of Escherichia coli–Shigella genetic exchange communities

2012
Open Biol
PMCID: 3472396
PMID: 23091700
DOI: 10.1098/rsob.120112

[…] details, including parameter value settings for Mauve, ProbCons, GBLOCKS and MrBayes, see [].Topological discordance between the MRP supertree and individual query (protein) trees was assessed using EEEP [] with a 95 per cent bootstrap collapse threshold and the strict reference treeratchet (-rR). Where an optimal solution could be found, EEEP reports the minimal set of subtree prune-and-regraft […]

library_books

DNA variation in the phenotypically diverse brown alga Saccharina japonica

2012
BMC Plant Biol
PMCID: 3490969
PMID: 22784095
DOI: 10.1186/1471-2229-12-108

[…] ious recombination detection methods implemented in the program RDP3 [] (Table ). The parental and recombinant sequences were determined using the VisRD method [], modified version of PHYLPRO [], and EEEP [] also implemented in RDP3 (default settings).All six methods detected a single recombination event in S. latissima within the 1,257 bp COI region (Figure A), with high statistical support (Tabl […]

Citations

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EEEP institution(s)
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia; ARC Centre in Bioinformatics, Australia; Advanced Computational Modelling Centre, The University of Queensland, Brisbane, Australia
EEEP funding source(s)
Supported by an operating grant from the Australian Research Council, and by the Australian Research Council's award of a Federation Fellowship.

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