BEAGLE 3.1.2 – Evaluating the Likelihood of Sequence Evolution on Trees

BEAGLE 3.1.2

:: DESCRIPTION

BEAGLE-lib (Broad-platform Evolutionary Analysis General Likelihood Evaluator) is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

::DEVELOPER

BEAGLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 BEAGLE 

:: MORE INFORMATION

Citation

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.
Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

PRAP 2.0b3 – Parsimony & Likelihood Ratchet Analysis with PAUP*

PRAP 2.0b3

:: DESCRIPTION

PRAP (Parsimony and likelihood ratchet analyses with PAUP*) allows the calculation of Bremer support (BS, Decay values; Bremer 1988) using the parsimony ratchet algorithm (Nixon, 1999). Alternatively, BS can also be computed without using the ratchet.In addition, simple Parsimony Ratchet searches can be performed with PRAP, also by superposing random addition cycles onto the published ratchet procedure (Nixon, 1999) to further decrease the slight risk that even the Ratchet gets stuck in a single series of cycles. Here, a series of ratchet iterations (commonly about 200 iterations) is repeatedly started from different starting trees, and shortest trees from all these iterations series are collected.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

PRAP

:: MORE INFORMATION

Citation

Müller K
The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support
BMC Evolutionary Biology 2005, 5:58

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.

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.

Mendel 14.3 – Likelihood-based Statistical Analysis

Mendel 14.3

:: DESCRIPTION

Mendel performs likelihood-based statistical analysis to solve a variety of genetic problems. Implementations are included for all common, and several novel, statistical genetic tests. Data sets can consist of qualitative or quantitative traits, pedigree or population samples, limited loci or dense SNPs. Where appropriate, the analysis will use either the Elston-Stewart or Lander-Green-Kruglyak algorithms, whichever is more efficient for each individual pedigree.

::DEVELOPER

Kenneth Lange  (mendel@genetics.ucla.edu)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Mendel

:: MORE INFORMATION

Citation:

Fast genome-wide pedigree quantitative trait loci analysis using MENDEL.
Zhou H, Zhou J, Sobel EM, Lange K.
BMC Proc. 2014 Jun 17;8(Suppl 1):S93. doi: 10.1186/1753-6561-8-S1-S93

Mendel: the Swiss army knife of genetic analysis programs.
Lange K, Papp JC, Sinsheimer JS, Sripracha R, Zhou H, Sobel EM.
Bioinformatics. 2013 Jun 15;29(12):1568-70.

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.

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.

MRVTEST 1.0 – Model-free Linkage Analysis using Likelihoods

MRVTEST 1.0

:: DESCRIPTION

MRVTEST is a simple program which automates setting up likelihood calculations for combined linkage and association analysis using a variety of different transmission models. It consists of an adaptation of the earlier MFLINK program, which performs likelihood-based model-free linkage analysis.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MRVTEST

:: MORE INFORMATION

Citation:

Curtis D, Sham PC. (1995)
Model-free linkage analysis using likelihoods.
Am J Hum Genet 57: 703-716.

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.

ALE 20130717 – Assembly Likelihood Estimator

ALE 20130717

:: 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.