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CopyCat specifications


Unique identifier OMICS_08811
Name CopyCat
Alternative name COPhYlogenetiC Analysis Tool
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.04
Stability Stable
Maintained Yes




No version available



  • person_outline Alexander Auch

Publication for COPhYlogenetiC Analysis Tool

CopyCat citations


Insect bacteria parallel evolution in multiple co obligate aphid association: a case in Lachninae (Hemiptera: Aphididae)

Sci Rep
PMCID: 5579299
PMID: 28860659
DOI: 10.1038/s41598-017-10761-9

[…] st–parasite association matrix. Each individual host–parasite association can also be tested. Two event-base methods (Jane 4.0 and TreeMap v1.0), and a distance-based method (ParaFit) implemented in CopyCat were used in this study. Phylogenetic relationships among the aphid species in Lachninae used in this study came from the study of Chen et al..In Jane, the following event-cost scheme was used […]


Cryptic diversity in Tranzscheliella spp. (Ustilaginales) is driven by host switches

Sci Rep
PMCID: 5335255
PMID: 28256543
DOI: 10.1038/srep43549
call_split See protocol

[…] tive per putative species. The host topology was obtained by PhyML analysis based on rbcL, ITS and trnH-psbA alignment of the representative specimens. For the distance-based analyses of cophylogeny, COPYCAT 2.02 was used, which incorporated a wrapper for ParaFit. The congruence between the host and parasites phylogenies were computed and statistical significance tests were assessed by comparing r […]


Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea

Front Microbiol
PMCID: 4789555
PMID: 27014209
DOI: 10.3389/fmicb.2016.00285
call_split See protocol

[…] t relationship and of interactions between individual links that contribute to the overall pattern. PACo was run in R-project (ver. 3.1.1) using the script provided by , and AxParaFit was run through CopyCat GUI (), both with 105 permutations. […]


Hidden biodiversity in an ancient lake: phylogenetic congruence between Lake Tanganyika tropheine cichlids and their monogenean flatworm parasites

Sci Rep
PMCID: 4558575
PMID: 26335652
DOI: 10.1038/srep13669

[…] een phylogenies without assuming congruence to be produced by cospeciation, and are hence considered less biased than topology-based methods. Distance-based cophylogenetic analysis was carried out in Copycat v.1.14 making use of AxParafit and AxPcoords using 9999 permutations under default settings. In this analysis, the independence between host and parasite patristic distances is tested. To this […]


Host Jumps and Radiation, Not Co‐Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae

PLoS One
PMCID: 4521919
PMID: 26230508
DOI: 10.1371/journal.pone.0133655
call_split See protocol

[…] ween host and parasite distances and do not test for the presence of any coevolutionary events. In this study, patristic distances (summed branch lengths along a phylogenetic tree) were calculated in CopyCat 2.02 [] for each host and parasite phylogeny. The global fit between trees is computed and tested by randomizing individual host-parasite associations. ParaFit was used to test whether a parti […]


The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin infecting begomoviruses in Mexico

Virus Evol
PMCID: 5014474
PMID: 27774278
DOI: 10.1093/ve/vev004

[…] cy of pseudorecombination in PepGMV and PHYVV populations was explored by analyzing the topological congruence between the maximum likelihood phylogenies of DNA-A and DNA-B of each virus. We used the CopyCat program (), which incorporates a wrapper for the program ParaFit (). ParaFit is a distance-based approach that assesses the fit between DNA-A and DNA-B phylogenetic distance matrices by transf […]


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CopyCat institution(s)
Center for Bioinformatics and Organismic Botany/Mycology, Tübingen, Germany; University of Tübingen, Tübingen, Germany
CopyCat funding source(s)
Financial support provided by the Deutsche Forschungsgemeinschaft.

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