Tag: fit

WH – Fit Speciation Model to DNA Sequence data sets

WH

:: DESCRIPTION

WH is a computer program that carries out the fitting of a speciation model, and conducts tests of the quality of fit of that model.  The speciation model is called the Isolation Model, and is one without gene flow.  With comparative DNA sequence data from each of two closely related species, the method allows an estimation of the time since speciation and the size of the ancestral species.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  WH

:: MORE INFORMATION

phylolm 2.6.2 – R package for Fitting Phylogenetic Linear Regression models

phylolm 2.6.2

:: DESCRIPTION

phylolm is an R package providing a function for fitting phylogenetic linear regression models. The likelihood is calculated with an algorithm that is linear in the number of tips in the tree. The package also provides a function for simulating continuous traits along the tree.

::DEVELOPER

Lam Si Tung Ho

:: REQUIREMENTS

  • Linux/windows/ MacOsX
  • R Package

:: DOWNLOAD

 phylolm

:: MORE INFORMATION

Citation

Syst Biol. 2014 Feb 4. [Epub ahead of print]
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
Ho LS, Ané C.

Myriads v1.2 – p-value-based Dependence Detection, Simulation, and multiple testing correction

Myriads v1.2

:: DESCRIPTION

Myriads (formerly SGoF+) is a software package for p-value-based multiple testing that also implements a dependence test and p-value simulation.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

Myriads

:: MORE INFORMATION

Citation

Carvajal-Rodriguez A (2018).
Myriads: p-value-based multiple testing correction.
Bioinformatics 34 (6): 1043-104 https://doi.org/10.1093/bioinformatics/btx746

Carvajal-Rodriguez A, Uña-Alvarez J (2011)
Assessing Significance in High-Throughput Experiments by Sequential Goodness of Fit and q-Value Estimation.
PLoS ONE 6(9): e24700

 

DaDi 1.6.3 – Fit Population Genetic Models using a Diffusion Approximation to the Joint Frequency Spectrum

DaDi 1.6.3

:: DESCRIPTION

DaDi (Diffusion Approximations for Demographic Inference) is a rapid and powerful diffusion method for fitting demographic models to genetic polymorphism data.

::DEVELOPER

Ryan Gutenkunst

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Python

:: DOWNLOAD

 DaDi 

:: MORE INFORMATION

TreeFit 20120420 – Evaluate How well a UPGMA or Neighbor-joining Tree fits a Genetic Distance Matrix

TreeFit 20120420

:: DESCRIPTION

TreeFit evaluates how well a UPGMA or neighbor-joining tree fits a genetic distance matrix.TreeFit was written to analyze how well a tree fits the genetic data the tree was calculated from. TreeFit creates neighbor-joining and UPGMA trees from a genetic distance matrix, and then compares the observed genetic distance between populations with the genetic distance in the tree. The similarity between these distances is express as R-squared, the familiar statistic used to summarize the scatter of points around a least-squares regression line.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 TreeFit

:: MORE INFORMATION

Citation

KALINOWSI ST (2009)
How well do evolutionary trees describe genetic relationships between populations?
Heredity 102:506-513.