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Supplementary toolbox

Data management and analysis tools
Genetics tools
Breeding decision tools
Molecular tools
Administration tool

Operative Systems: Windows    Macintoch    Solaris     Linux

# Programs with functions that won't be included in the IBP workbench

Experimental Design

Plant Data Management

Variance Analysis

Genetic Analysis of Germplasms

Genetic Mapping

QTL Mapping

Breeding Tools

Gene/Marker conversion

Project Management

Tool Function User-friendly          System         
EDGAR Create Excel templates for experimental design with one or two treatment factors. ****
GDPC Genomic Diversity and Phenotype Connection. Import data (germplasm collection, pedigrees, loci, environmental experiment, phenotype) and retrieve data from public databases (Gramene rice, wheat and maize; Panzea). ***
Flapjack Genotyping data management. Visualize large genotyping dataset for all types of molecular markers, SNP haplotype, position on chromosome map and co-localization with QTL. ****
OpenStat Statistical software. Include descriptive analyses (frequency, error, normality test, boxplots), comparative tests, anova, regressions, non-parametric tests, calculation and data transformation. **
DARwin Analyse diversity and phylogeny of germplasms on the basis of evolutionary dissimilarities and genotyping data. Useful to select parents of segregating population. *
Structure Investigate population structure using genotyping data. Infer the presence of distinct populations, assign individuals to populations, study hybrid zones, identify migrants and admixed individuals. To use prior association mapping study. *
MapDisto Construct genetic map of molecular markers. Add molecular markers to a pre-existing map. Calculate distortion of segregation, multi-point order of the markers, simple QTL analysis. Export map in QGene format. ****
TetraploidMap Construct genetic map of molecular markers for autotetraploid genomes. ****
CSSL Finder# 
Manage introgression lines for developing Chromosome Segment Substitution Lines (CSSLs). ****
MapChart Produce charts of genetic linkage maps and QTL data for comparative mapping. Highly customizable. Wide-scale QTL visualization on genetic map. Comparison possible with physical map (BAC contigs, deletion bin maps...). ***
MergeMap Construct consensus genetic map from individual maps **** Webtool
QGene Simple and sophisticated QTL analyses. Visualize data distribution, produce mathematical transformation of phenotypic data. Execute single and multi-trait analyses, single-environment analysis. Perform QTL analysis for metabolome data. QTL chart per linkage group. Import from MapDisto. ****
ICIM ICIM (QTL IciMapping) is a software to construct genetic linkage map and map QTL by simple interval mapping and inclusive composite interval mapping. It can also map segregation distorsion loci, analyse QTL by environment interaction in biparental populations, and map QTL in Nested Association Mapping populations. ****
BioMercator Compare genetic maps and QTL position between independent experiments for meta-QTL analysis. ***
TASSEL Evaluate traits associations, evolutionary patterns and linkage disequilibrium. Association mapping using General Linear Model and Mixed Linear Model. Include GDPC. Import data from FlapJack. *** Webtool, standalone
QU-GENE Simulation program to investigate the characteristics of genetic material undergoing repeated cycles of selection and marking. **
DNA Subway#
From a DNA sequence, identify the orthologous sequences in model species (Blast, sequence alignment, phylogenic tree, annotation). **** Webtool, standalone
Design primers in conserved region between sequences of  your crop and the model species, in order to amplify intron, more prone to contain polymorphism. **** Webtool, standalone
NovoSNP# Identify SNP and InDel in sequencing projects. Automatically read trace files (Sanger sequencing), orientate the sequence in same direction, align against a reference sequence and list the sequence variations. Output is SNP or Indel type and position. Can also clip and annotate sequences. ***
GanttProject# Make Gantt chart, show percentage complete bar, add tasks and milestones, assign personnel and resources. Project file can be saved in .xml format and shared on a server with username and password. ****
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