CoRe-PA is a tool for reconstructing the coevolutionary history of host parasite systems. As Tarzan it uses an event-based method to find cost minimal reconstructions. These events are cospeciation, sorting, duplication and (host)switching.

With CoRe-PA you can:

  • design host parasite scenarios with a graphical editor
  • generate random coevolutionary scenarios using the beta-split model with beta 0, -1 or -1.5
  • generate random coevolutionary scenarios by simulating coevolution
  • generate random coevolutionary scenarios which “keep the character” of given host parasite systems
  • handle non-binary host and parasite phylogenies
  • choose between different behaviors of how to handle switches
  • use divergence timing information
  • compute the best reconstructions for a given set of costs
  • compute the best cost vector for a given host parasite system (where the cost vector fits best to the reconstructed event frequencies)
  • do randomization tests for given host parasite systems to analyze the probability of coevolution
  • export host parasite scenarios and their reconstructions to svg

CoRe-PA 0.5.2 Downloads

CoRe-PA for Linux 32bit
CoRe-PA for Linux 64bit
CoRe-PA for Windows 32bit
CoRe-PA for Windows 64bit
CoRe-PA for MacOS 32bit
CoRe-PA for MacOS 64bit
Sample data

Simple command line version which can be executed by “java -jar core-pa_cli_0.5.2.jar -i inputfile -o outputfile -a”.

Command line version for randomization tests which can be executed by java -jar core-pa_rnd_0.5.2.jar -i inputfile -o outputfile. A tutorial for CoRe-PA can be found here.

CoRe-PA is an Eclipse RCP application. You don’t need to install the software. Just unzip the archive to a local folder and run the core-pa executable. Java 1.5 or later has to be installed on your system.

Please note that this is an beta release and there may exist several bugs in the software. So feel free to send bug reports or any other kind of impressions or suggestions on CoRe-PA to

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CoRe-PA Publications

Reference for CoRe-PA:

D. Merkle, M. Middendorf, N. Wieseke
A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies
BMC Bioinformatics 2010, 11(Suppl 1):S60, 2010

Paper where CoRe-PA is used for cophylogenetic analysis:

G. Ozawa, S. Shimamura, Y. Takaki, K. Takishita, T. Ikuta, J. P. Barry, T. Maruyama, K. Fujikura, T. Yoshida
Ancient Occasional Host Switching of Maternally Transmitted Bacterial Symbionts of Chemosynthetic Vesicomyid Clams
Genome Biology and Evolution, 9(9): 2226–2236, 2017.

S. J. Anthony, C. K. Johnson, D. J. Greig, S. Kramer, X. Che, H. Wells, A. L. Hicks, D. O. Joly, N. D. Wolfe, P. Daszak, W. Karesh, W. I. Lipkin, S. S. Morse, PREDICT Consortium, J.A.K. Mazet,.T. Goldstein
Global patterns in coronavirus diversity
Virus Evolution , 3(1): vex012, 2017.

J. Mélade, N. Wieseke, B. Ramasindrazana, O. Flores, E. Lagadec, Y. Gomard, S. M. Goodman, K. Dellagi, H. Pascalis
An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism
Sci Rep. 6: 23752, 2016

Y. Gomard, M. Dietrich, N. Wieseke, B. Ramasindrazana, E. Lagadec, S.M. Goodman, K. Dellagi, P. Tortosa
Malagasy bats shelter a considerable genetic diversity of pathogenic Leptospira suggesting notable host-specificity patterns
FEMS Microbiology Ecology, 92(4):fiw03, 2016

C.S. Herrera, Y. Hirooka, P. Chaverri
Pseudocospeciation of the mycoparasite Cosmospora with their fungal hosts
Ecology and Evolution, 6(5): 1504–1514, 2016.

Y.-J. Choi, M. Thines
Host Jumps and Radiation, Not Co-Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae.
PLoS ONE 10(7): e0133655, 2015.

K. O’Donnella, S. Sinka, R. Libeskind-Hadasb, J. Hulcrc, M. T. Kassond, R. C. Ploetze, J. L. Konkole, J. N. Ploetze, D. Carrilloe, A. Campbelle, R. E. Duncane, P. N.H. Liyanagef, A. Eskaleng, F. Nag, D. M. Geiserh, C. Batemanc, S. Freemani, Z. Mendeli, M. Sharoni, T. Aokij, A. A. Cossék, A. P. Rooney
Discordant phylogenies suggest repeated host shifts in the Fusarium–Euwallacea ambrosia beetle mutualism
Fungal Genetics and Biology, 82:277-90, 2015

Y. Zhang, S. Zhang, Y. Li, S. Ma, C. Wang, M. Xiang, X. Liu, Z. An,J. Xu, X. Liu
Phylogeography and evolution of a fungal – insect association on the Tibetan Plateau
Molecular Ecology, 23: 5337–5355, 2014

D. Santiago-Alarcon, A. Rodríguez-Ferraro, P. G. Parker, R. E. Ricklefs
Different meal, same flavor: cospeciation and host switching of haemosporidian parasites in some non-passerine birds
Parasites & Vectors, 9: 286, 2014

M. Rosenblueth, L. Sayavedra, H. Sámano-Sánchez,A. Roth, E. Martínez-Romero
Evolutionary relationships of flavobacterial and enterobacterial endosymbionts with their scale insect hosts (Hemiptera: Coccoidea)
Journal of Evolutionary Biology, 25(11): 2357-2368, 2012, DOI: 10.1111/j.1420-9101.2012.02611.x

D. Coulibaly-N’Golo, B. Allali, S.K. Kouassi, E. Fichet-Calvet, B. Becker-Ziaja, et al.:
Novel Arenavirus Sequences in Hylomyscus sp. and Mus (Nannomys) setulosus from Côte d’Ivoire: Implications for Evolution of Arenaviruses in Africa.
PLoS ONE 6(6): e20893, 2011. doi:10.1371/journal.pone.0020893

N. Du Toit, B. J. Van Vuuren, S. Matthee and C. A. Matthee
Biogeography and host-related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts
Molecular Ecology, 22(20): 5185-5204, 2013, doi: 10.1111/mec.12459

A. Levitsky
The Utility of Standardized DNA Markers in Species Delineation and Inference of the Evolutionary History of Symbiotic Relationships in the Malagasy Ant Melissotarsus insularis Santschi, 1911 and its Scale Associate (Diaspididae)
Master Thesis, The University of Guelph, 2013

K. Nemirov, H. Leirs, Å. Lundkvist, G. E. Olsson
Puumala hantavirus and Myodes glareolus in northern Europe: no evidence of co-divergence between genetic lineages of virus and host
J Gen Virol 91 (2010), 1262-1274

M. Dilcher, L. Hasib, M. Lechner, N. Wieseke, M. Middendorf, M. Marz, A. Koch, M. Spiegel, G. Dobler, F. T. Hufert, M. Weidmann
Genetic Characterisation of Tribec virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses
Virology , 423(1): 68-76, 2012

M. L. Forister, C. R. Feldman
Phylogenetic Cascades and the Origins of Tropical Diversity
BIOTROPICA, 43(3): 270-278, 2011.