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CoRe-PA specifications


Unique identifier OMICS_08812
Name CoRe-PA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Daniel Merkle

Publication for CoRe-PA

CoRe-PA citations


Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

Mol Ecol
PMCID: 5900718
PMID: 29421852
DOI: 10.1111/mec.14523
call_split See protocol

[…] To detect potential codivergence patterns, we tested for cophylogeny between fungal species and host family trees with CoRe‐PA 0.5.1 (Merkle, Middendorf, & Wieseke, ), PACo (Balbuena, Míguez‐Lozano, & Blasco‐Costa, ) and Jane 4 (Conow, Fielder, Ovadia, & Libeskind‐Hadas, ) as these programs can accommodate pathogens w […]


Ancient Evolution of Mammarenaviruses: Adaptation via Changes in the L Protein and No Evidence for Host–Virus Codivergence

Genome Biol Evol
PMCID: 5863214
PMID: 29608723
DOI: 10.1093/gbe/evy050
call_split See protocol

[…] iruses are unknown and these viruses were thus not included in the analyses.Cophylogeny between mammarenaviruses and their natural hosts was investigated with two event-based methods, Jane 4.0 () and CoRe-PA version 0.5.1().The phylogenetic tree of rodents was obtained from a previous work () and derives from the concatenation of 5 nuclear genes. The phylogeny also included two hosts from differen […]


FISSA: A neuropil decontamination toolbox for calcium imaging signals

Sci Rep
PMCID: 5823956
PMID: 29472547
DOI: 10.1038/s41598-018-21640-2

[…] e.For the data in Fig. , all surgical and imaging procedures are detailed in our previous publication. Briefly, adeno-associated viruses (AAV1.Syn.GCaMP6f.WPRE.SV40, University of Pennsylvania Vector Core, PA, USA) were locally injected in V1 at three different depths (−50, −400, and −600 μm) in 8 mice (8- to 10-week-old). The mice were obtained by crossing Cre-driver transgenic mice lines (Sst


Myocardial Scar Delineation Using Diffusion Tensor Magnetic Resonance Tractography

PMCID: 5850260
PMID: 29420216
DOI: 10.1161/JAHA.117.007834

[…] normal from infarcted myocardium, with good correlation to late gadolinium enhancement and endocardial voltage mapping.Normal myocardium (PA ≤4), border zone (PA values between 4 and 10), and infarct core (PA >10) had progressively more myofiber heterogeneity.Delineation of infarct regions using PA correlated well with that based on late gadolinium enhancement and endocardial voltage mapping. We i […]


Ancient Occasional Host Switching of Maternally Transmitted Bacterial Symbionts of Chemosynthetic Vesicomyid Clams

Genome Biol Evol
PMCID: 5604134
PMID: 28922872
DOI: 10.1093/gbe/evx166

[…] lly congruent positions of the seven host-symbiont pairs (P < 0.05; BF > 5; table 3 and ; orange branches).Coevolution analyses between host clams and their symbionts were performed with Jane 4.0 and CoRe-PA. The Jane 4.0 analysis estimated three coevolution patterns, of which two were selected by our criteria described in the Materials and Methods section (). CoRe-PA yielded six coevolution patte […]


Global patterns in coronavirus diversity

Virus Evol
PMCID: 5467638
PMID: 28630747
DOI: 10.1093/ve/vex012

[…] ost switching, and failure to diverge (or sorting) (; ), which are used to create a minimal-cost reconstruction of the evolutionary history between the viruses and hosts. Another cophylogeny program, CoRe-PA (), uses a parameter-adaptive approach to estimate an appropriate cost scheme without any prior value assignment. For our analysis, we used Jane with the default pre-determined cost scheme whe […]


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CoRe-PA institution(s)
Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark; Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Germany

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