HIERFSTAT 0.5-10 – Package for R to Compute & Test Hierarchical F-statistics

HIERFSTAT 0.5-10

:: DESCRIPTION

HIERFSTAT is a package for R allowing to estimate F-statistics and variance components with the methods of moments for any number of levels in a hierarchy. The package also allows to test the significance of population differentiation using the likelihood ratio G-statistic or the variance components.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HIERFSTAT

:: MORE INFORMATION

Citation

Goudet, J. (2005)
Hierfstat, a package for R to compute and test hierarchical F-statistics.
Molecular Ecology Notes. 5: 184-186

HybridNet – Compute rSPR Distances, Hybridization Numbers, and Hybridization Networks

HybridNet

:: DESCRIPTION

 HybridNet is a programs for computing the rSPR distance , a maximum agreement forest (MAF) , all maximum agreement forests (MAFs) , the hybridization number , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two given phylogenetic trees. Once our programs find an MAAF, they also construct an optimal hybridization network .

::DEVELOPER

Chen Lab  & Lusheng Wang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 HybridNet

:: MORE INFORMATION

Citation

HybridNET: a tool for constructing hybridization networks.
Chen ZZ, Wang L.
Bioinformatics. 2010 Nov 15;26(22):2912-3. doi: 10.1093/bioinformatics/btq548.

BiodivR 1.2 – Compute Statistically Unbiased Indices of Species Diversity

BiodivR 1.2

:: DESCRIPTION

BiodivR is designed to characterise species diversity within samples as well as species similarity between samples using sub-sampling (rarefaction) procedures. The statistics proposed account for the non-exhaustive sampling of species to get estimates unbiased with respect to the sizes (numbers of individuals recorded) of the samples.

::DEVELOPER

Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   BiodivR

:: MORE INFORMATION

Patristic – Input different Tree files and computes their Patristic Distances

Patristic

:: DESCRIPTION

Patristic is a Java program that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

Patristic

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  Patristic

:: MORE INFORMATION

Citation

Fourment M, Gibbs MJ.
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change.
BMC Evol BIOl. 2006; 6:1

QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies

QUANTO 1.2.4

:: DESCRIPTION

Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.

::DEVELOPER

The Division of Biostatistics @ usc.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

Heritability Calculator – Compute Heritability for different Genetic Architectures

Heritability Calculator

:: DESCRIPTION

Heritability Calculator (HC) is a comprehensive package enabling the calculations of epidemiological and genetic parameters (such as broad/narrow sense heritabilities, true and population based heritability estimates, familial relative risk, marginal and epistatic effect size, detection power) for general (non-additive) genetic architectures.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Matlab

:: DOWNLOAD

 Heritability Calculator

:: MORE INFORMATION

Citation

The Mystery of Missing Heritability: Genetic Interactions Create Phantom Heritability 
O. Zuk, E. Hechter, S. Sunyaev and E.S. Lander
Proceedings of the National Academy of Science (2012) doi: 10.1073/pnas.1119675109

Melting 5.2.0 – Compute Nucleic Acid Duplex Melting Temperature

Melting 5.2.0

:: DESCRIPTION

Melting computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program first computes the hybridisation enthalpy and entropy from the elementary parameters of each Crick’s pair by the nearest-neighbor method. Then the melting temperature is computed. The set of thermodynamic parameters can be easely changed, for instance following an experimental breakthrough.

MELTING provides a large set of thermodynamic models to compute the enthalpy and entropy of several structures in the duplex : perfectly matching sequences, single mismatch, tandem mismatch, internal loop, single dangling end, second dangling end, long dangling end (only one to four poly A), single bulge loop, long bulge loop, inosine base (I), hydroxyadenine (A*), azobenzene (cis X_C and trans X_T), locked nucleic acids (Al, Gl, Tl, Cl).

::DEVELOPER

Melting team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Melting

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 16;13:101. doi: 10.1186/1471-2105-13-101.
MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
Dumousseau M1, Rodriguez N, Juty N, Le Novère N.

DNAux 3.0 – Generate Random DNA Sequences & Compute Overlapped Sequence

DNAux 3.0

:: DESCRIPTION

DNAux is a software package that includes a Random Generator Tool to generate a lists of random elements in a text file (such as DNA sequences) and a Sliding Window Sequences Generator to compute a list of partially overlapped sequences from any DNA sequence.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNAux

:: MORE INFORMATION

Citation

Pereira F, Soares P, Carneiro J, Pereira L, Richards M, Samuels DC, Amorim A
Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region
Molecular Biology and Evolution. 2008. 25: 2759–2770

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

Reputer – Compute and Visualize Repeat Structures

Reputer

:: DESCRIPTION

The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes.

::DEVELOPER

Prof. Dr. Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux

:: DOWNLOAD

 Reputer

:: MORE INFORMATION

Citation

S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich:
REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale.
Nucleic Acids Res., 29(22):4633-4642, 2001.