Natural Variation & QTL Tool Kit

Tools and resources for researchers interested in ecotypes, accessions, natural variation and QTLs in Arabidopsis.

1001 Genomes Project

Homepage of the 1001 Genomes Project for Arabidopsis thaliana, which aims to to discover the whole-genome sequence variation in 1001 strains Arabidopsis thaliana to link phenotipic diversity with genome variation.

Abstract: Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. 

Arabidopsis lyrata

Arabidopsis Lyrata database with BLAST tool, keyword search, and map viewer. 


An automated CAPS marker based genotyping system. 

dCAPS finder

Programme to design PCR primers for dCAPs markers.

From the abstract: Here we describe a web-based program, dCAPS Finder 2.0, that facilitates the design of mismatched PCR primers to create or remove a restriction endonuclease recognition site relative to the polymorphism being analyzed.

Genetic Analysis Software

A comprehensive listing of genetic analysis software held at Rockefeller.


Standalone application for: 1) Displaying genetic maps and QTL through a graphical user interface; 2) Performing automatic compilations of several genetic maps through a projection process; 3) Computing meta-analysis of QTL detected in independent experiments.

From the abstract: BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface.


Software application for QTL mapping in multi-cross design.

From the abstract: This paper addresses an issue common to all QTL mapping methods, that of determining an appropriate threshold value for declaring significant QTL effects. An empirical method is described, based on the concept of a permutation test, for estimating threshold values that are tailored to the experimental data at hand. The method is demonstrated using two real data sets derived from F(2) and recombinant inbred plant populations.


GWAPP is a web application for genome-wide association mapping in Arabidopsis. 

From the abstract: Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.

Marker Tracker

Contains computationally generated CAPS markers across 96 accessions, and 152 enzymes, from Arabidopsis.


Search for SNPS between arbitrary groups of ecotypes/accessions.

From the abstract: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design.

NASC Ecotype Search

Searchable database of Arabidopsis ecotypes. Search options include 'altitude' and 'phenotype.'

Nordborg lab

Tools and resources for genome wide association mapping and comparative genomics in Arabidopsis.

TAIR Ecotype Search

Searchable database of ecotypes and Arabidopsis relatives.

TAIR Polymorphism Search

Search for SNPs and visible polymorphisms in chromosomal region of interest.