LEADMIX 1.0 – Likelihood Estimation of ADMIXture

LEADMIX 1.0

:: DESCRIPTION

LEADMIX is a Fortran program to estimate the admixture proportions and genetic drift using data on genetic markers

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Fortran 90/95 compiler

:: DOWNLOAD

 LEADMIX

:: MORE INFORMATION

Citation

Wang, J. (2003)
Maximum Likelihood Estimation of Admixture Proportions from Genetic Data.
Genetics 164: 747-765.

GeLL 2.0 – General Likelihood Library for use in Phylogenetics

GeLL 2.0

:: DESCRIPTION

GeLL is a General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques.

::DEVELOPER

Daniel Money

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 GeLL

:: MORE INFORMATION

Citation

GeLL: A Generalized Likelihood Library for Phylogenetic Models.
Money D, Whelan S.
Bioinformatics. 2015 Feb 27. pii: btv126.

KinCohort – Likelihood-based analysis of Kin-cohort data

KinCohort

:: DESCRIPTION

KinCohort is a MATLAB software package for likelihood-based analysis of kin-cohort data.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Matlab

:: DOWNLOAD

 KinCohort

:: MORE INFORMATION

Citation

A marginal likelihood approach for estimating penetrance from kin-cohort designs.
Chatterjee N and Wacholder S.
Biometrics. 2001 Mar;57(1):245-52.

Coala 1.2.1 – COevolution Assessment by a Likelihood-free Approach

Coala 1.2.1

:: DESCRIPTION

Coala is an algorithm for estimating the frequency of the events based on an approximate Bayesian computation approach.

::DEVELOPER

ERABLE (European Research team in Algorithms and Biology, formaL and Experimental)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 Coala

:: MORE INFORMATION

Citation

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, and M.-F. Sagot.
Cophylogeny reconstruction via an approximate Bayesian computation.
Systematic Biology, 2014, doi:10.1093/sysbio/syu129.

zipHMM 1.0.1 – Library for very fast Likelihood Computations for Hidden Markov Models

zipHMM 1.0.1

:: DESCRIPTION

zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 zipHMM

:: MORE INFORMATION

Citation:

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A, Kristiansen M, Pedersen CN, Mailund T.
BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.

UNCcombo 0.1 – Likelihood based Association Testing for NGS data without intermediate Genotype Galling

UNCcombo 0.1

:: DESCRIPTION

UNCcombo is a R package to perform single marker association testing on raw next generation sequencing data.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX
  • R

:: DOWNLOAD

 UNCcombo

:: MORE INFORMATION

Citation

Likelihood Based Complex Trait Association Testing for Arbitrary Depth Sequencing Data.
Yan S, Yuan S, Xu Z, Zhang B, Zhang B, Kang G, Byrnes A, Li Y.
Bioinformatics. 2015 May 14. pii: btv307.

SWALO – Scaffolding with Assembly Likelihood Optimization

SWALO

:: DESCRIPTION

SWALO is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

::DEVELOPER

Pachter Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  •  Bowtie 2

:: DOWNLOAD

SWALO

:: MORE INFORMATION

 

GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

LIME 0.2-1 – Likelihood approach for detecting Imprinting and Maternal Effects

LIME 0.2-1

:: DESCRIPTION

LIME is a partial Likelihood approach for detecting Imprinting and Maternal Effects (LIME) using nuclear families with an arbitrary number of affected and unaffected children.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LIME

:: MORE INFORMATION

Citation

Yang, J. and Lin, S. (2012)
Robust Partial Likelihood Approach for Detecting Imprinting and Maternal Ects Using Case-Control Families.
Annals of Applied Statistics, in press. DOI: 10.1214/12-AOAS577.

ALE 20180904 – Assembly Likelihood Estimator

ALE 20180904

:: DESCRIPTION

ALE is a probabalistic framework for determining the likelihood of an assembly given the data (raw reads) used to assemble it. It allows for the rapid discovery of errors and comparisons between similar assemblies.

::DEVELOPER

Scott Clark@Cornell University Center for Applied Mathematics, Rob Egan@Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • C Compiler
  • Python

:: DOWNLOAD

 ALE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):435-43. doi: 10.1093/bioinformatics/bts723. Epub 2013 Jan 9.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Clark SC, Egan R, Frazier PI, Wang Z.