'Ready to use' software

The GCP has contributed to the development of a wide array of software packages, databases or webbased facilities. This material is newly developed or adapted software, intended for the GCP crop scientists and breeders. On this page you will find links to these products. The contribution of the Generation Challenge Programme to their development varies from support for translation to complete funding.

The GCP has both ready to use software packages and on-line facilities, listed below.

The on-line software programmes and facilities, which sometimes require large computing power, are accessible via the High Performance Computing grid.

•    Dayhoff - a comparative stress gene catalog
  
  
The GCP has developed Dayhoff, the ortholog gene catalogue. (http://202.123.56.214:8080/DayhoffWeb2/) Dayhoff documents stress-responsive genes comparatively across plant species. It is a compendium of protein families, phylogenetic trees and multiple sequence alignments with the associated experimental evidence. It serves to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought’). For example, the comparison of microarray data about drought stress obtained across diverse crop species can be analysed in a comparative manner to identify common gene expression profiles under similar stresses. The web site includes query and visualization tools and allows searches and browsing of the underlying project database. (read more)


•   GreenPhylDB - a phylogenomic database for plant comparative genomics
  
  GreenPhylDB is a phylogenomic database for plant comparative genomics. GreenPhylDB offers the most complete plant family list and is manually curated. The major part of these families have been analyzed with the CIRAD optimized phylogenomic pipeline. In addition, GreenPhylDB includes GOST (GreenPhyl Orthologs Search Tool) to predict phylogenomic relationships between any plant sequence gene and O.sativa /A.thaliana gene(s).
  
  
•   GOST - GreenPhyl orthologs search tool


GOST (GreenPhyl Orthologs Search Tool) is a web site developed by GCP to predict phylogenomic relationships between any plant gene and Oryza sativa and / or Arabidopsis thaliana gene(s). GOST rapidly infers ortholog relationships by integrating a new sequence into a model phylogeny developed on these plant species. GOST is based on GreenphylDB, a phylogenomic database for plant comparative genomics and the most complete plant family list manually curated. GreenPhylDB is the comprehensive platform for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes.  


•   DARwin - Dissimilarity Analysis and Representation for Windows


DARwin (Dissimilarity Analysis and Representation for Windows) is a popular, well designed software package developed by GCP. It offers diversity and phylogenetic analysis. Nucleic sequences, amino acid sequences, molecular markers, and qualitative or quantitative characters can be utilised to infer and transform dissimilarity matrices. Different algorithms are available for factorial analyses, tree construction and the accession of their reliability. Several trees based on the same data set can be compared. Ease readible graphics can be made. 


•   iMAS - Integrated Marker-Assisted Selection System


The Integrated Marker-Assisted Selection System (iMAS) software is an integrated molecular breeding analysis platform. The GCP supported the development of the iMAS. The iMAS provides simple-to-follow guidelines to assist users with the selection of the most appropriate experimental design and data analysis methods. It offers the users a regularly updated selection of the currently most appropriate options. The iMAS performs the required reformatting of datasets for all included software.


•   DIVA-GIS - a geographic information system


DIVA-GIS is a free and open source geographic information system (GIS) to make maps of species distribution data and analyze these data.  DIVA-GIS 6.0.3 was specifically developed by GCP at CIP for use with genebank data such as available through national or international genebank documentation systems and SINGER, the System-wide Information Network for Genetic Resources the germplasm information exchange network of the CGIAR and partners. The DIVA-GIS program is particularly useful for mapping and analyzing biodiversity data, such as the distribution of species. A program with a similar name and comparible functionalities. DIVA-GIS version 5.4, was indepently developed from the historic DIVA-GIS source code files. The two programmes are not compatible.   


•   CMTV - Comparative Map and Trait Viewer


The Comparative Map and Trait Viewer (CMTV) is tool for constructing consensus maps and comparing QTL and functional genomics data across genomes and experiments. The CMTV is a graphical user interface developed for constructing complex visualizations of genetic and genomic data collected from a variety of sources. It was designed to provide researchers with an intuitive mechanism to compare and integrate their own local mapping data with data from public databases, as well as to enable the aggregation of data from disparate sources into a common representational framework.  GCP supported the development of  this program into an open source Java code.  (brochure) (read more) 


•   RiCES - Rice Cis-Element Searcher


RiCES is a cis-element searching tool optimized for rice (Oryza sativa) genome. It takes as input a list of identifiers of transcription unit IDs of Oryza sativa, defined in Pseudomolecule corresponding to KOME full length cDNA clones, and returns a list of cis-element sites that appear to be shared across the listed gene loci. The motif searching program, MEME, is applied in the front step of the analysis. The RiCES tool is available as webservice. (read more)


•   RiceGeneThresher 2.0 - interface to find the stress-responsive genes and their location


RiceGeneThresher is a web-based application for mining genes underlying QTLs in the Rice genome. RiceGeneThresher incorporated the “The Generation Challenge Programme Comparative Plant Stress-responsive Gene Catalogue” on http://dayhoff.generationcp.org/ for an online resource documenting stress-responsive genes comparatively across plant species (Wanchana, Thongjuea et al. 2008). RiceGeneThresher provides user friendly interface to find the stress-responsive genes and their location in the genome region of interest. 


•   OryGenesDB - an interactive tool for rice reverse genetics


The OryGenesDB CIRAD-based webservice originated from the the Oryza sativa database.
Sequence information is linked with related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc). Data sources are available for rice (spp. indica and spp. japonica, sorghum and Arabidopsis. A genome Browser (Gbrowse), displaying genomic annotations and other features, is the core of this database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. A set of tools around GBrowse was developed to retrieve as exhaustively as possible information related to queries with several starting points.
In addition, Orylink can be found on this website, offering a personal and integrated system for functional genomic analysis.


•   GenDiversity - combining decentralised genotyping data for diversity analysis


GenDiversity, a webservice developed at CIRAD, is a query and analysis application which combines genotyping data from several data sources, developed in support of diversity studies.
GenDiversity offers different functionalities: querying genotyping data from different databases (the GCP Central Registry, Tropgene, IRIS), combining two or more different genotyping studies, filtering by passport data, computation of allelic frequencies, computation of LD, and checking for duplicates. Gendiversity can convert the outputs to the file format of choice, suitable for diversity analysis (DARwin, Convert, Structure, Haploview). 

 

• The FREQS-R Program estimates allele frequencies for fingerprinting and genetic diversity studies using bulked heterogeneous populations.
  FREQS-R  converts peak heights of SSR alleles run on a DNA sequencer into frequencies of the alleles within the bulk of individuals amplified with the SSR.  FREQS-R is a freely available program written using the R software. It was written as a simplified R version of the MSSC - SAS®/IML program (Dubreuil et al. 2005; Franco et al. 2005).
  Find here the user's manual for the applicable for the FREQ-S program.
  The freely available R version of the FREQ-S program can be found here. The FREQS-R program must be copied as a script into the R default directory and called using icons at Windows. 
  
  
• The FtoL-R Program estimates the allele lengths of “dummy” data set of individuals, using the frequencies of marker-allele combinations from bulk populations. The FtoL-R program was written to convert frequencies of SSR alleles run on an DNA sequencer for bulks of n individuals into length of alleles of n simulated individuals, hypothetically belonging to the bulk.  The allele frequencies of the hypothetical individuals are the same as the allele frequencies of the bulk. The FtoL program generates a “dummy” data set consisting of allele lengths for hypothetical individuals. These individuals correspond to bulk populations and are generated using the frequencies of marker-allele combinations from the bulks.
  Find here the user's manual for the applicable for FtoL analysis progam.
  The freely available R version of the FtoL program can be found  here. This FtoL-R program must be copied as a script into the R default directory, and generally called using icons in Windows
  
  
• Core Hunter is a  tool for sampling genetic resources from a reference data set and for establishing core subsets.
  Users can specify the sampling intensity, which genetic measures will be used for selection criteria, or both.
  Diverse types of subsets can be created, either based on preferences for allele representativeness or for allele richness.

• Haplophyle,  is developed for phylogeographic analysis. The analysis of haplotype networks is combined with geographic data. Haplophyle thus reconstructs genealogies based on haplotypes, in relation to geographic patterns. The identification of predominant haplotypes is based on the analysis of polymorphisms. In addition the interference of ancestral haplotypes and recombination can be discerned.


More analytic software is available via the High Performance Computing grid.

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