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.

MCPeP – Monte Carlo Simulations of Peptide-membrane Interactions

MCPeP

:: DESCRIPTION

The MCPep server is designed for non-experts wishing to perform Monte Carlo (MC) simulations of helical peptides in association with lipid membranes.

::DEVELOPER

Polymer Research Center , The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Monte Carlo simulations of peptide-membrane interactions with the MCPep web server.
Gofman Y, Haliloglu T, Ben-Tal N.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W358-63. doi: 10.1093/nar/gks577.

MCell 3.3 – Monte Carlo Simulator of Cellular Microphysiology

MCell 3.3

:: 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.

MORGAN 3.3 – Monte Carlo Genetic Analysis

MORGAN 3.3

:: 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.

MCPerm 1.1.4 – A Monte Carlo Permutation method for Multiple Test Correlation

MCPerm 1.1.4

:: DESCRIPTION

MCPerm is a Monte Carlo permutation method for multiple test correlation.

::DEVELOPER

Yongshuai Jiang <jiangyongshuai at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 MCPerm

:: MORE INFORMATION

Citation

MCPerm: a Monte Carlo permutation method for accurately correcting the multiple testing in a meta-analysis of genetic association studies.
Jiang Y, Zhang L, Kong F, Zhang M, Lv H, Liu G, Liao M, Feng R, Li J, Zhang R.
PLoS One. 2014 Feb 21;9(2):e89212. doi: 10.1371/journal.pone.0089212. e

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

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