Markov

Forward Viterbi algorithm based on the Python code found at: http://en.wikipedia.org/wiki/Viterbi_algorithmAlso included is an example based on the one from the Wikipedia page for a simple 2-state model with 4 observations. To paraphrase:Bob tells Alice his daily activities (observations) and... Platforms: Matlab

MesoRD is a tool for stochastic simulation of reactions and diffusion [2]. In particular, it is an implementation of the Next Subvolume Method [3, 4], which is an exact method to simulate the Markov process corresponding to the reaction-diffusion master equation [5, 6, 7]. Since version 0.2.0... Platforms: *nix

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies... Platforms: *nix

Flack Overstow allows you to create StackOverflow "spam" messages by using Markov chains to randomize recent posts by a given user. Uses StackApps API v0.8. Platforms: *nix

MegaHAL is a 'conversation simulator' that learns as you talk to it. MegaHAL differs from conversation simulators such as Eliza in that it uses a Markov Model to learn how to hold a conversation. It is possible to teach MegaHAL to talk about new topic Platforms: *nix

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =... Platforms: *nix

The system can be scripted and embedded, and includes integrated instrument libraries, post-tonal and microtonal pitch modeling tools, multiple-format graphical outputs, and musical output in Csound, SuperCollider, Pure Data, MIDI, audio file, XML, and text formats. Musical parts are deployed as... Platforms: Windows, Mac, *nix, Python, BSD Solaris

DadaDodo project is a program that generates random sentences based on input files. Sometimes these sentences are nonsense; but sometimes they cut right through to the heart of the matter, and reveal hidden meanings. DadaDodo works rather differently than Dissociated Press; whereas... Platforms: *nix

Acme::Wabby is a Perl extension used to create semi-random sentences based upon a body of text. This module is used to create semi-random sentences based on a body of text. It uses a markov-like method of storing probabilities of word transitions. It is good for annoying people on IRC, AIM, or... Platforms: *nix

Benzo is a blabberbot written in python. His means of generating text is a Markov Chain- an algorithm that takes english text as input, and generates output (when addressed) based on statistics gathered from the input text. At least thats what its used for here. Just a few notes about version... Platforms: *nix

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the... Platforms: Mac

Petri Net Editor is a small, easy to use, Java based application specially designed to offer users an editor for stochastic Petri-nets. This tool is designed to also allow you to create reachability trees and Markov graphs, simulate and gather statistics on simulation. for WindowsAll Platforms: Windows

ClaMS is a handy application specially designed to offer you a sequence composition-based classifier for metagenomic sequences. ClaMS works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov... Platforms: Windows

libDAI is a handy C++ library designed to offer implementations of various inference methods for discrete graphical models. libDAI supports arbitrary factor graphs with discrete variables; this includes discrete Markov Random Fields and Bayesian Networks. The library is targeted at researchers.... Platforms: Windows

Lzip is a lossless data compressor based on the LZMA algorithm, with very safe integrity checking and a user interface similar to the one of gzip or bzip2. Lzip decompresses almost as fast as gzip and compresses better than bzip2, which makes it well suited for software distribution and data... Platforms: Mac, Linux

The Automatic Model Optimization Reference Implementation, AMORI, is a framework that integrates the modelling and the optimization processes by providing a plug-in interface for both. A genetic algorithm and Markov simulations are currently implemented. Platforms: Windows, Mac, Linux

D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites. Platforms: Windows, Mac, Linux

SediStat is simple command line aplication for automatization of statistical calculations used in facial analysis of deep water sediments. In actual version are incorporated methods of R/S analysis and Markov chains computations. Platforms: Windows, Mac, Linux

HapCluster is a software package for linkage disequilibrium mapping.It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. Platforms: C and C plus plus

Introduction to Stochastic Search and Optimization is an overview of the principles, algorithms, and practical aspects of stochastic optimization, including applications drawn from engineering, statistics, and computer science. The book may serve as either a reference book for researchers and... Platforms: Matlab