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.

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

PLEX 0.95 – Phylogenetics, Likelihood, Evolution, and CompleXity

PLEX 0.95

:: DESCRIPTION

The PLEX package is designed to perform rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • R package

:: DOWNLOAD

 PLEX

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2989-90. doi: 10.1093/bioinformatics/bts555. Epub 2012 Sep 12.
Phylogenetics, likelihood, evolution and complexity.
de Koning AP, Gu W, Castoe TA, Pollock DD.

IPHULA / pIPHULA 1.16 – Inference of Population History Using a Likelihood Approach

IPHULA / pIPHULA 1.16

:: DESCRIPTION

IPHULA / pIPHULA (parallel Inference of Population History Using a Likelihood Approach) is a software that investigates parameters of population history based on a Monte Carlo simulation using the maximum likelihood framework.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX

:: DOWNLOAD

 IPHULA / pIPHULA

:: MORE INFORMATION

Citation:

H.A. Schmidt, A. von Haeseler, and J. Buschbom (2007)
pIPHULA – Parallel Inference of Population Parameters Using a Likelihood Approach.
Bioinformatics (2007) 23 (19): 2636-2637.

PedPeel 0.0.2 – Prepare Pedigree data for Calculation of Elston-Stewarts’ Likelihood function

PedPeel 0.0.2

:: DESCRIPTION

PedPeel prepares pedigree data for calculation of Elston-Stewarts’ likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 PedPeel

:: MORE INFORMATION

Citation:

Comput Biol Chem. 2007 Jun;31(3):173-7. Epub 2007 Mar 24.
Optimal peeling order for pedigrees with incomplete genotypic information.
Belonogova NM, Axenovich TI.

ECLIPSE 1.1 – Error Correcting Likelihoods In Pedigree Structure Estimation

ECLIPSE 1.1

:: DESCRIPTION

ECLIPSE (Error Correcting Likelihoods In Pedigree Structure Estimation) is a set of three programs (preproc, eclipse2 and eclipse3) which analyze genetic marker data for genotyping and/or pedigree errors. Using the same preprocessing program (preproc) eclipse2 analyzes data on pairs of individuals, while eclipse3 analyzes data jointly of trios.

::DEVELOPER

Elizabeth A. Thompson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 ECLIPSE

:: MORE INFORMATION