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CarthaGene specifications


Unique identifier OMICS_33268
Name CarthaGene
Alternative name CARHTA GENE
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Version 1.2
Stability Stable
Registration required Yes
Maintained Yes


No version available


  • person_outline Thomas Schiex

Publication for CarthaGene

CarthaGene citations


Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number

Front Plant Sci
PMCID: 5862827
PMID: 29599793
DOI: 10.3389/fpls.2018.00333
call_split See protocol

[…] hosen to represent this bin. If there was no missing date of the markers in one bin, one marker was chosen randomly. SNP markers and the previously mapped 59 SSR markers were sorted into groups using Carthagene (). LOD thresholds between 5.0 and 10.0 and a threshold of genetic distance of 80 cM were tested to reach an optimum marker number in linkage groups. The linkage map was constructed using t […]


Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements

J Genomics
PMCID: 5744233
PMID: 29290830
DOI: 10.7150/jgen.23222

[…] lture DNA Midi Kit (Qiagen, Hilden, Germany). Genotyping reactions were carried out on a Fluidigm platform using the BioMark 96.96 Dynamic Array for gene-expression analysis, as described previously .CarthaGène software was used to perform two-point linkage analyses and to determine the marker order and inter-marker distances in centiRays (cRs). CarthaGène looks for multiple populations' maximum- […]


Contributions of Zea mays subspecies mexicana haplotypes to modern maize

Nat Commun
PMCID: 5707364
PMID: 29187731
DOI: 10.1038/s41467-017-02063-5

[…] th traits were used for QTL mapping.All the TM lines and their parents were genotyped using the Illumina MaizeSNP50 array. To construct the genetic linkage map, a method was developed integrating the Carthagene software in a Linux system with in-house Perl scripts ( Markers that completely co-localized were assigned into a chromosomal bin. Each bin was c […]


QTL seq analysis identifies two genomic regions determining the heading date of foxtail millet, Setaria italica (L.) P.Beauv.

Breed Sci
PMCID: 5790050
PMID: 29398946
DOI: 10.1270/jsbbs.17061

[…] ified products of the Indel markers and digested products of the CAPS markers were electrophoresed in 3% and 1.5% agarose gel to detect polymorphisms, respectively.Linkage maps were constructed using CarthaGene (version 1.2.3) with a Haldane mapping function (). Markers were assigned to linkage groups using the “group” command with an LOD = 3.0 and a map distance below 30 cM. QTL analysis was carr […]


High‐resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa‐5A

Plant Biotechnol J
PMCID: 5902775
PMID: 29024288
DOI: 10.1111/pbi.12850

[…] Genetic maps of DH, NI‐RIL, RS‐NIL3 and RH‐CS populations/panels were constructed using CarthaGène 1.2‐LKH (de Givry et al., ). Maps of RS‐NIL3 and RH‐CS panel were initially calculated using the algorithm for a haploid model, as haploid data sets allow faster ordering of the marker data […]


Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening

BMC Plant Biol
PMCID: 5649070
PMID: 29052528
DOI: 10.1186/s12870-017-1116-1

[…] from the FUxPAZ2 RILpopulation was used for mapping. A set of SSR markers and additional SNPs from candidate genes sequencing was added to the “AXIOM” markers. A consensus map was then built with the CARTHAGENE software (, []) in using mergen command. In the process of obtaining robust consensus map, we used a) the markers mapped in [], b) and from the AXIOM arra […]


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CarthaGene institution(s)
INRA, Biométrie et Intelligence Artificielle/Génétique Cellulaire, Castanet-Tolosan, France
CarthaGene funding source(s)
Supported by GENOPLANTE project ‘Integrative Tools for Genetic Mapping’.

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