BYPASSR 1.0 / BYPASSR-DEGR 1.0.2 – Bayesian Phylogenetic Analysis of Site-Specific Rate / with a model for Post Mortem Modification

BYPASSR 1.0 / BYPASSR-DEGR 1.0.2

:: DESCRIPTION

BYPASSR is the implementation of a new method for inferring branch lengths and site-specific substitution rates from nucleotide sequences. It makes use of the Bayesian Markov Chain Monte Carlo method and of the uniformization (randomization) technique to calculate sequence substitution probabilities in complicated DNA substitution models such as general time reversible model (GTR).

BYPASSRdegr is a software packages for estimating degradation levels of ancient DNA sequences

::DEVELOPER

Ligia M. Mateiu MD PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
C/C++ Compiler

:: DOWNLOAD

BYPASSR , BYPASSR-DEGR

:: MORE INFORMATION

Citation

Syst Biol. 2006 Apr;55(2):259-69.
Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation.
Mateiu L, Rannala B.

Bayesian inference of errors in ancient DNA caused by postmortem degradation.
Mateiu LM, Rannala BH.
Mol Biol Evol. 2008 Jul;25(7):1503-11.

BayeSSC – Bayesian Serial SimCoal

BayeSSC

:: DESCRIPTION

BayeSSC is a modification of SIMCOAL 1.0. BayesSSC is powerful because it allows flexible coalescent modelling from a variety of different priors. The enables parameter estimation, likelihood calculations, and Bayesian inference. Typically, BayeSSC generates thousands of hypothetical trees using slightly different population parameters. The simulated genetics of these trees can then be compared to the actual genetics of the user’s samples to investigate which history of these many simulated histories is the most likely to have generated the samples.

::DEVELOPER

The Hadly Lab at Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX / Window

:: DOWNLOAD

BayeSSC

:: MORE INFORMATION

Citation

Excoffier, Novembre, Schneider (2000),
“SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography“,
Journal of Heredity, 91:506-509.

K-Pax – Bayesian unsupervised Classification of Protein Sequences

K-Pax

:: DESCRIPTION

K-Pax contains an implementation of a Bayesian model-based method for simultaneously classifying aligned proteins into functionally divergent subgroups and identifying their function specific residues

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
Matlab

:: DOWNLOAD

K-Pax

:: MORE INFORMATION

Citation:

Marttinen, P., Corander, J., Törönen, P. and Holm, L. (2006).
Bayesian search of functionally divergent protein subgroups and their function specific residues.
Bioinformatics, 22, 2466-2474.

BLink 3.0 – compute Linkage Disequilibrium based on a Bayesian estimate of D’

BLink 3.0

:: DESCRIPTION

BLink (Bayesian Linkage) is a software to compute linkage disequilibrium based on a bayesian estimate of D’

::DEVELOPER

Bios, University of GranadaGranada , Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

BLink

:: MORE INFORMATION

Citation:

Sebastiani P.; Abad-Grau M.M.
“Bayesian estimates of Linkage Disequilibrium”
BMC Genetics, 8, 1-13, 2007

CryoBayes beta – Bayesian method for Inferring 3D structure of Macromolecules

CryoBayes beta

:: DESCRIPTION

CryoBayes is a Bayesian method for inferring 3D structure of macromolecules imaged by Electron Cryo-Microscopy experiments. We encourage experimental Structural Biologists to download and try our code. We hope that our technique will be useful as a method of automatically generating intial models given only class average images.

::DEVELOPER

Lilien Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

CryoBayes

:: MORE INFORMATION

Citation:

Jaitly, N., Brubaker, M.A., Rubinstein, J.L. and Lilien, R.H.
A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy,
Bioinformatics, 26(19):2406-15 (2010).

PHASE 2.0 – Bayesian & Maximum Likelihood Phylogenetic Inference Package

PHASE 2.0

:: DESCRIPTION

PHASE (PHylogenetics And Sequence Evolution) is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.

::DEVELOPER

Rattray Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

PHASE

:: MORE INFORMATION

Citation

V. Gowri-Shankar and M. Rattray.
A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model” Molecular Biology and Evolution
Molecular Biology and Evolution 24(6):1286-1299 (2007).

Bayes Aligner – Bayesian Adaptive Sequence Alignment Software

Bayes Aligner

:: DESCRIPTION

Bayes Aligner is a bayesian adaptive sequence alignment algorithms.Instead of requiring a fixed set of parameter settings, this algorithm returns the Bayesian posterior probability for the number of gaps and for the scoring matrices in any series of interest. Furthermore, instead of returning the single best alignment for the chosen parameter settings, this algorithm returns the posterior distribution of all alignments considering the full range of gapping and scoring matrices selected, weighing each in proportion to its probability based on the data.

::DEVELOPER

Brown University Center for Computational Molecular Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/Solaris sparc

:: DOWNLOAD

Bayes Aligner

:: MORE INFORMATION

Citation

Zhu, J.;Liu, J.S.; Lawrence, C.E.
Bayesian adaptive sequence alignment algorithms.
Bioinformatics 14:25-39, 1998

PrIME-GSR 1.0 – Bayesian Integrated Model

PrIME-GSR 1.0

:: DESCRIPTION

primeGSR is a program for gene tree inference that takes a known species tree into account. It is based on GSR, a probabilistic model integrating gene duplication, sequence evolution and a relaxed molecular clock for substitution rates, and efficient algorithms that enables genome-wide analysis of gene families.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PrIME-GSR

:: MORE INFORMATION

Citation:

Åkerborg, Sennblad, Arvestad, Lagergren, Gene tree analysis using a Bayesian integrated model for genes, sequences, and rates, submitted.