LICENCE CONTACT REGISTRATION
| IMPUTE v2.3.0 04-01-2013 |
a program for genotype imputation and phasing
in genome-wide association studies and fine-mapping studies based on a dense set of marker data (such as 1000 Genomes Project haplotypes) Marchini et al. (2007) Nature Genetics 39 : 906-913, Howie et al. (2009) PLoS Genetics 5(6): e1000529. Marchini et al. (2010) Nature Reviews Genetics 11, 499-511 Howie et al. (2011) G3 1(6) 457-470. Howie et al. (2012) Nature Genetics 44, 955–959. |
 |
| SNPTEST v2.5 (beta) 13-06-2013 |
a program for Frequentist and Bayesian tests
of SNP association with binary (case-control) and
quantitative phenotypes that takes genotype uncertainty
into account. Marchini et al. (2010) Nature Reviews Genetics 11, 499-511 |
 |
| SHAPEIT v2 04-12-2012 |
a
program for accurate and efficient phasing of genetic
datasets Delaneau et al. (2012) Nature Methods 9, 179–181. [SuppMat] Delaneau et al. (2013) Nature Methods 10, 5-6. [SuppMat] ASHG 2012 Presentation Thursday, Nov 8 11:00AM ASHG 2012 Poster 1484 Wed, Nov 7, 3:15-4:15PM |
 |
| HAPGEN v2.2.0 01-04-2011 |
a program to simulate case control datasets at
linked SNP markers conditional upon a set of known
haplotypes. Spencer et al. (2009) PLoS Genetics 5(5). Su et al. (2011) Bioinformatics 27 (16) 2304-2305. |
 |
| GWAPOWER |
an
R package for assessing the power of genome-wide
association studies using commercially available
genotyping chips. The package encapsulates extensive
simulation results generated by our program HAPGEN
and described fully in the paper Spencer et al. (2009) PLoS Genetics 5(5) |
|
| MULTIMIX v1.1.0 06-11-2012 |
a
program for admixture deconvolution using multiple (i.e.
> 2) phased or unphased ancestral panels. Churchhouse and Marchini (2012) Genet Epidem DOI: 10.1002/gepi.21692 ASHG 2012 Poster 3384 Thur, Nov 8, 3:15-4:15PM |
 |
| MVNCALL v1.0.0 17-10-2012 |
a
program for genotype calling and phasing using
next-generation sequencing reads and a haplotype scaffold. Menelaou and Marchini (2012) Bioinformatics doi:10.1093/bioinformatics/bts632. ASHG 2012 Presentation Thursday, Nov 8 11:15AM |
 |
| META v.1.5.0 29-03-2013 |
a program to carryout meta-analysis of genetic
studies. Liu et al. (2010) Nature Genetics 42, 436–440. |
 |
| GENECLUSTER v1.0.0 19-03-2012 |
a program for location and detection of
unobserved causal loci in fine-mapping experiments and
genome-wide association studies. Su et al. (2009) Statistical Science 24(4) 430-450. |
 |
| CHIAMANTE v1.0.0 24-07-2012 |
a joint genotype calling algorithm for array
and sequence data. This method can be used to call
genotype from just array data. O'Connell and Marchini (2012) Genet Epi 36: 527–537 |
 |
| CHIAMO v0.2.1 22-10-2007 |
a genotype calling algorithm for multi-cohort
studies. |
 |
| QCTOOL v1.3 |
a
program for carrying out SNP and sample quality control
(QC) for genome-wide association studies |
|
| GTOOL v0.7.5 05-04-2012 |
a program for (a) generating
subsets of genotype data, and (b) converting genotype data
between the PED file format and the FILE FORMAT used by
SNPTEST and IMPUTE. |
| Genetics Software Suite,
(c) 2007, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). The Genetics Software Suite consists of the software CHIAMO, GTOOL, IMPUTE, SNPTEST, HAPGEN, GENECLUSTER, BIA, HAPQUEST The Software is distributed "AS IS" under this Licence solely for non-commercial use in the hope that it will be useful, but in order that the University as a charitable foundation protects its assets for the benefit of its educational and research purposes, the University makes clear that no condition is made or to be implied, nor is any warranty given or to be implied, as to the accuracy of the Software, or that it will be suitable for any particular purpose or for use under any specific conditions. Furthermore, the University disclaims all responsibility for the use which is made of the Software. It further disclaims any liability for the outcomes arising from using the Software. The Licensee agrees to indemnify the University and hold the University harmless from and against any and all claims, damages and liabilities asserted by third parties (including claims for negligence) which arise directly or indirectly from the use of the Software or the sale of any products based on the Software. No part of the Software may be reproduced, modified, transmitted or transferred in any form or by any means, electronic or mechanical, without the express permission of the University. The permission of the University is not required if the said reproduction, modification, transmission or transference is done without financial return, the conditions of this Licence are imposed upon the receiver of the product, and all original and amended source code is included in any transmitted product. You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions. You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference DP3507. |