CSI – Construct Confidence set of Markers within prespecified Genetic Distance from the Disease Locus

CSI

:: DESCRIPTION

CSI (confidence set inference) uses affected sib pairs data and relative risks to construct a confidence set of markers within a prespecified genetic distance from the disease locus.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CSI

:: MORE INFORMATION

Citation

Papachristou, C., Lin, S. (2006)
Microsatellites Versus Single-Nucleotide Polymorphisms in Confidence Interval Estimation of Disease Loci.
Genetic Epidemiology, 30, 3-17.

ILPMap 20110128 – Construct Consensus Genetic Maps under Comparative Analysis

ILPMap 20110128

:: DESCRIPTION

ILPMap is a software of constructing consensus genetic maps in comparative analysis.

::DEVELOPER

Chen Xin , Yang Jian-Yi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
IBM ILOG CPLEX

:: DOWNLOAD

ILPMap

:: MORE INFORMATION

Citation

X. Chen and J. Yang.
Constructing Consensus Genetic Maps in Comparative Analysis.
J Comput Biol. 2010 Nov;17(11):1561-73. Epub 2010 Oct 20.

MSTMap – Construct Genetic Linkage Maps

MSTMap

:: DESCRIPTION

MSTMap is a software tool that is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool builds the genetic linkage map by first constructing a Minimum Spanning Tree (MST), and hence the name MSTMap. The algorithm implemented in MSTMap is very efficient and can handle ultra-dense maps of up to 10,000~100,000 markers. According to our experimental studies, when the data quality is high, the accuracies of the maps produced by our tool are as good as those by the best tools available in the literature. However, when the data are noisy, the maps generated by our algorithm are significantly better.

MSTMap Online

::DEVELOPER

Yonghui Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GraphViz

:: DOWNLOAD

MSTMap

:: MORE INFORMATION

Citation:

PLoS Genet. 2008 Oct;4(10):e1000212. Epub 2008 Oct 10.
Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph.
Wu Y, Bhat PR, Close TJ, Lonardi S.

MergeMap – Construct Accurate Consensus Genetic Map

MergeMap

:: DESCRIPTION

MergeMap is a software tool that is capable of constructing accurate consensus genetic maps from a set of individual genetic maps. The input to MergeMap, a set of individual maps, are first converted to DAGs internally, which are then merged into a consensus graph on the basis of shared vertices. Conflicts among the individual maps will be shown as cycles in the consensus graph. MergeMap tries to resovle conflicts by deleting a minimum set of marker occurrences. The details about the conflicts as well the decision by MergeMap are shown to the user graphically. The result of this conflict-resolution step is a consensus DAG, which will be simplified and then linearized to produce the final consensus map.

MergeMap Online Version

::DEVELOPER

Yonghui Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GraphViz

:: DOWNLOAD

MergeMap

:: MORE INFORMATION

Citation:

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):381-94.
Accurate construction of consensus genetic maps via integer linear programming.
Wu Y, Close TJ, Lonardi S.

ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool

ConStruct 3.2.5

:: DESCRIPTION

ConStruct (construction of RNA consensus structures) is an RNA alignment editor and consensus structure prediction tool. It combines multiple sequence alignment, thermodynamic structure prediction and statistics in a semiautomatical fashion. Its sophisticated GUI guides the user through correcting an initial sequence alignment with respect to a consensus structure.

::DEVELOPER

Gerhard Steger <steger@biophys.uni-duesseldorf.de>,Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Universitätsstr

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

ConStruct

:: MORE INFORMATION

Citation:

Wilm, A., Linnenbrink, K. & Steger, G. (2008)
ConStruct: improved construction of RNA consensus structures.
BMC Bioinformatics 9, 219.