LEA / parLEA – Likelihood-based Estimation of Admixture

LEA / parLEA

:: DESCRIPTION

LEA (Likelihood-based estimation of admixture)is a program to simultaneously estimate admixture and the time since admixture

parLEA is a parallelized version of LEA.

::DEVELOPER

the Population and Conservation Genetics group , parLEA Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

LEA / parLEA

:: MORE INFORMATION

Citation

Langella, Chikhi, Beaumont (2001),
“LEA (Likelihood-based estimation of admixture): a program to simultaneously estimate admixture and the time since admixture“,
Molecular Ecology Notes, 1(4):357-358.

A novel parallel approach to the likelihood-based estimation of admixture in populatin genetics
Ambra Giovannini; Gaetano Zanghirati; Mark A. Beaumont; Lounes Chikhi; Guido Barbujani
Bioinformatics 2009 25: 1440-1441

Distance 1.0 – Estimation of Reversible Substitution Matrices and Evolutionary Distance

Distance 1.0

:: DESCRIPTION

Distance is a program written by Lars Arvestad that implements a least-squares method for estimating general reversible DNA substitution matrices and evolutionary distances.

::DEVELOPER

William J. Bruno and Lars Arvestad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Complier

:: DOWNLOAD

Distance

:: MORE INFORMATION

Citation

J Mol Evol. 1997 Dec;45(6):696-703.
Estimation of reversible substitution matrices from multiple pairs of sequences.
Arvestad L, Bruno WJ.

FluxEs 2.0 – Metabolic Flux Estimation

FluxEs 2.0

:: DESCRIPTION

FluxEs is a program for metabolic flux analysis using NMR spectra of tracer experiments.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Unix

:: DOWNLOAD

FluxEs

:: MORE INFORMATION

FluxEs 1.0 is freely available via web interface. FluxEs 2.0 is a development version and will be made available via web interface upon request.

BARCE 1.2 – Bayesian Application for Recombination and Gene Conversion Estimation

BARCE 1.2

:: DESCRIPTION

BARCE (Bayesian Application for Recombination and Gene Conversion Estimation) is a C++ program for detecting recombination breakpoints in four-sequence alignments using hidden Markov models, Bayesian principles and Markov chain Monte Carlo sampling.

::DEVELOPER

Grainne McGuire and Dirk Husmeier

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
C++ compiler

:: DOWNLOAD

BARCE

:: MORE INFORMATION

Citation

Husmeier D., McGuire G. (2003):
Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo,
Molecular Biology and Evolution 20(3):315-337.

Leaphy 1.0 beta – Phylogenetic Tree Estimation Software

Leaphy 1.0 beta

:: DESCRIPTION

Leaphy (Likelihood Estimation Algorithms in Phylogenetics) uses maximum likelihood (ML) to estimate trees from aligned amino acid and nucleotide sequences under a variety of commonly used and popular models.

::DEVELOPER

Simon Whelan

:: REQUIREMENTS

Windows / Linux / MacOSX

:: DOWNLOAD

Leaphy

:: MORE INFORMATION

Citation

S. Whelan.
New approaches to phylogenetic tree search and their application to large numbers of protein alignments.
Syst Biol (2007) 56 (5): 727-740. doi: 10.1080/10635150701611134