Tag: Fast

FastMap 2.0 – Fast Association Mapping in Heterozygous Populations

FastMap 2.0

:: DESCRIPTION

FastMap is a software for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide polymorphisms (SNPs). In particular, SNPs are organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required to calculate the association of a SNP by making use of the association of its parent SNP in the tree. FastMap’s tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.

::DEVELOPER

Carolina Center for Computational Toxicology

:: SCREENSHOTS

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 FastMap

:: MORE INFORMATION

Citation

D.M. Gatti, A.A. Shabalin, T.C. Lam, F.A. Wright, I. Rusyn, and A.B. Nobel.
FastMap: Fast eQTL mapping in homozygous populations.
Bioinformatics, 25(4):482, 2009.

HappieClust 1.6.1 – Fast Approximate Hierarchical Clustering using Similarity Heuristics

HappieClust 1.6.1

:: DESCRIPTION

HappieClust is an approximate version of agglomerative hierarchical clustering. When performing the standard full agglomerative hierarchical clustering, each pair of objects must be inspected to evaluate similarity. This is very time-consuming for large numbers of objects and/or complicated similarity measures. HappieClust performs agglomerative hierarchical clustering with partial information, not requiring all pairwise similarities to be known. HappieClust is further able to use similarity heuristics to carefully choose a subset of pairs for which the similarities are evaluated.

::DEVELOPER

Meelis Kull, Jaak Vilo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX

:: DOWNLOAD

 HappieClust

:: MORE INFORMATION

Citation

M. Kull, J. Vilo. .
Fast approximate hierarchical clustering using similarity heuristics.
BioData Mining 2008, 1:9 (22 September 2008)

FAST 20070903 – Fourier Transform based Algorithms for Significance Testing of ungapped Multiple Alignments

FAST 20070903

:: DESCRIPTION

FAST (Fourier transform based Algorithms for Significance Testing of ungapped multiple alignments) is an open-source C/C++ package of programs and associated libraries for evaluating ungapped multiple alignments.

:: DEVELOPER

Uri Keich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C Compiler

:: DOWNLOAD

 FAST

:: MORE INFORMATION

Citation:

Bioinformatics. 2008 Feb 15;24(4):577-8. Epub 2008 Jan 6.
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.
Nagarajan N, Keich U.

 

Treephyler 1.1 – Fast Taxonomic Profiling of Metagenomes.

Treephyler 1.1

:: DESCRIPTION

Treephyler is a tool for fast taxonomic profiling of metagenomes. It combines the predictive power of tree-based and speed of signature-based approaches. Treephyler was evaluated on a real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Treephyler

:: MORE INFORMATION

Citation

F. Schreiber, P. Gumrich , R. Daniel and P. Meinicke (2010)
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics 26, 960-961