Phylo-SMC r0 – Bayesian Phylogenetic Inference tool based on Sequential Monte Carlo

Phylo-SMC r0

:: DESCRIPTION

Phylo-SMC is a Bayesian phylogenetic inference tool based on Sequential Monte Carlo (SMC), an alternative to the standard Markov Chain Monte Carlo approach (MCMC).

::DEVELOPER

Alexandre BouchardSriram Sankararaman, and Michael I. Jordan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX / Windows
  • Java
  • Phylip
  • Mrbayes
  • R package

:: DOWNLOAD

 Phylo-SMC

:: MORE INFORMATION

Citation

Syst Biol. 2012 Jul;61(4):579-93. doi: 10.1093/sysbio/syr131.
Phylogenetic inference via sequential Monte Carlo.
Bouchard, A., Sankararaman, S., Jordan, M.I

MateSim 1.0 – Monte Carlo Simulation of Mating

MateSim 1.0

:: DESCRIPTION

MateSim is a C++ computer program that implements Monte Carlo simulation models for generating mating tables under discrete or continuous traits. MateSim allows for different processes of pair formation and individual mutual mating propensity or preference models. It includes effects as drift, time dependent behaviour and ageing.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

MateSim

:: MORE INFORMATION

Citation

Carvajal-Rodríguez, A. 2018.
Monte Carlo simulation for the generation of mating tables.
BioSystems 171: 26-30 Doi: 10.1016/j.biosystems.2018.07.001.

MORGAN 3.4 – Monte Carlo Genetic Analysis

MORGAN 3.4

:: DESCRIPTION

MORGAN (Monte Carlo Genetic Analysis) is a collection of programs and libraries developed at the University of Washington under the PANGAEA (Pedigree Analysis for Genetics and Epidemiological Attributes) umbrella. This software implements a number of methods for the analysis of data observed on members of a pedigree, with the main programs implementing Markov Chain Monte Carlo (MCMC) methods.

::DEVELOPER

Elizabeth A. Thompson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MORGAN 

:: MORE INFORMATION

Citation:

E. A. Thompson (1995)
Monte Carlo in Genetic Analysis.
Technical report No. 294, Department of Statistics, University of Washington.

E. A. Thompson (2000)
Statistical Inferences from Genetic Data on Pedigrees
NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6. IMS, Beachwood, OH.

MCell 4.0.1 – Monte Carlo Simulator of Cellular Microphysiology

MCell 4.0.1

:: DESCRIPTION

MCell (Monte Carlo cell) is a program that uses spatially realistic 3-D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells—cellular microphysiology.

::DEVELOPER

MCell Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Mac OsX / Windows

:: DOWNLOAD

MCell

:: MORE INFORMATION

Citation:

Stiles, JR, and Bartol, TM. (2001).
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell.
In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127.

PhyloSim 3.0.5 – Monte Carlo Simulation of Sequence Evolution

PhyloSim 3.0.5

:: DESCRIPTION

PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloSim

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 19;12:104.
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.

GFMCMC 1.0 – C Library of GLUT for Markov Chain Monte Carlo

GFMCMC 1.0

:: DESCRIPTION

GFMCMC (GLUT for Markov Chain Monte Carlo) This is a library of C code that I wrote to use the (relatively) platform-independent OpenGL Utilities Toolkit (GLUT) for rendering pictures of one’s MCMC simulation in real time. It is essentially a small application programming interface.

::DEVELOPER

Eric C. Anderson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • C Compiler

:: DOWNLOAD

 GFMCMC

:: MORE INFORMATION

MCLEEPS 1.1 – Monte Carlo Likelihood Estimation of Effective Population Size

MCLEEPS 1.1

:: DESCRIPTION

MCLEEPS (Monte Carlo Likelihood Estimation of Effective Population Size) is a program for estimating effective population size from temporal changes in allele frequencies

::DEVELOPER

Eric Anderson and Ellen Williamson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MCLEEPS

:: MORE INFORMATION

Citation:

Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples
Eric C. Anderson, Ellen G. Williamson, and Elizabeth A. Thompson
Genetics, 156: 2109-2118. (December 2000)

Loki 2.4.5 – Monte Carlo analysis of multiple QTL

Loki 2.4.5

:: DESCRIPTION

Loki is a package developed by Simon C. Heath. Loki analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci.

::DEVELOPER

Simon Heath

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Loki 

:: MORE INFORMATION