Pure Python library for Hidden Markov Models
Anti-Spam SMTP Proxy Server implements multiple spam filters
The Anti-Spam SMTP Proxy (ASSP) Server project aims to create an open source platform-independent SMTP Proxy server which implements auto-whitelists, self learning Hidden-Markov-Model and/or Bayesian, Greylisting, DNSBL, DNSWL, URIBL, SPF, SRS, Backscatter, Virus scanning, attachment blocking, Senderbase and multiple other filter methods. Click 'Files' to download the professional version 2.6.1 build 18128. An linux and a freeBSD based OVA of ASSP V2 are also available for download. NOTICE...
JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
Java Modelling Tools is a suite for performance evaluation and modelling. Queuing Network models are solved with analytical, asymptotic and simulation methods; workload is characterized using clustering techniques.
An OpenSource Least-Squares-Adjustment Tool
JAG3D is no longer developed at source-forge, and has moved to GitHub. Please visit https://github.com/loesler/applied-geodesy or https://software.applied-geodesy.org to get the latest version.
Scientific computing, machine learning and computer vision for .NET
The Accord.NET Framework provides machine learning, mathematics, statistics, computer vision, computer audition, and several scientific computing related methods and techniques to .NET. The project is compatible with the .NET Framework. NET Standard, .NET Core, and Mono.
HMM and directed graph consensus combing error-correction tool
Frame-Pro is a tool using Hidden Markov Model and directed acyclic graph to correct the errors in DNA sequencing reads.
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes.
Probabilistic natural mapping for gene based association study.
PALM is a software that conducts gene-based association analysis. PALM exploits Hidden Markov Models (HMM) to capture the inner genomic structures. Then, unique gene features (termed "palm prints") are extracted for each gene set by calculating the natural gradient. Then palm-prints are tested with chi-square significance test.
Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines. TagDust allows users to specify the expected architecture of a read and converts it into a hidden Markov model. The latter can assign sequences to a particular barcode (or index) even in the presence of sequencing errors. Sequences not matching the architecture...
A tool for directed ortholog search in ESTs and proteins
HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel sequences from the search taxon.
Software for molecular simulations and trajectory analysis
We are proud to introduce version 3 of CAMPARI. This is a big step from version 2 primarily due to the comprehensive OpenMP (threads parallelism) support and due to significant improvements in both usability and performance. We have also again added a number of new algorithms from the recent literature, and CAMPARI of course continues to support the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in...
This package implements the algorithm bagging markov random field method with c++ together with Java interface. http://nar.oxfordjournals.org/content/41/2/e42.long Cytoscape App: BMRF-Net-CytoscapeV1.0.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-CytoscapeV1.0.tar.gz/download Source code and standalone version: BMRF-Net-standalone.tar.gz https://sourceforge.net/projects/bmrfcjava/files/BMRF-Net%20Package/BMRF-Net-standaloneV1.1.tar.gz/download BMRF-Net...
MLPACK is a C++ machine learning library with emphasis on scalability, speed, and ease-of-use. Its aim is to make machine learning possible for novice users by means of a simple, consistent API, while simultaneously exploiting C++ language features to provide maximum performance and flexibility for expert users. For more information, see http://mlpack.org
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. Sensitivity is gained by repeatedly running the HMM gene...
GUI for building, simulating and optimizing kinetic models.
A 3D graphical interface for building, simulating and optimizing Markov kinetic models in response to user defined time dependent stimuli. Models can be represented as either states and connecting transitions or interacting allosteric elements (see http://dx.doi.org/10.1085/jgp.201411183). Model parameters can be optimized by fitting model responses to user data. Optional user defined constraint equations for model parameters are parsed with EigenLab (https://github.com/marcel-goldschen-ohm...
J Usage Model Builder Library
JUMBL is a command line app and Java library that supports automation of model-based statistical testing. It supports creation, management, and application of usage models in the form of finite state Markov chains.
hiddenDomains: a modern HMM to identify ChIP-seq enrichment
hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities.
variational Bayes single particle tracking
vbSPT is an acronym for variational Bayes single particle tracking, a software package for hidden Markov Model analysis of single particle tracking data, primarily for biophysical applications. Journal reference: Extracting intracellular diffusive states and transition rates from single-molecule tracking data. Fredrik Persson, Martin Lindén, Cecilia Unoson & Johan Elf. Nature Methods (2013). doi:10.1038/nmeth.2367 http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2367.html
The KReator project is a collection of software systems, tools, algorithms and data structures for logic-based knowledge representation. Currently, it includes the software systems KReator and MECore and the library Log4KR: - KReator is an integrated development environment (IDE) for relational probabilistic knowledge representation languages such as Bayesian Logic Programs (BLPs), Markov Logic Networks (MLNs), Relational Maximum Entropy (RME), First-Order Probabilistic Conditional Logic...
Logi (Local Observations to Global Integration) transforms several local coordinate systems (composed of polar measurements) into a global spatial uniform network with respect to the Guide to the Expression of Uncertainty in Measurement (GUM).
Continuous time Markov chain (CTMC) can be used to describe describe the number of molecules and the number of reactions at any given time in a chemical reaction system. Gillespie algorithm is an important stochastic simulation algorithm, used to simulate each reaction track events of continuous time Markov chain in the number of collision frequency and collision time, but the computational cost is inevitably. In this project, Gillespie’s algorithm with rejection sampling introduces...
estimate population ancestry frequencies in admixed populations
This program uses discriminant analysis and Markov chain Monte Carlo to infer local ancestry frequencies in an admixed population from genomic data. This is done in the context of a continuous correlated beta process model that accounts for expected autocorrelations in local ancestry frequencies along chromosomes. This method is best-suited for the analysis of admixed populations that experience little or no on-going gene flow from the parental populations, but that are still segregating...
The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.
A hidden Markov model to predict clustered RNA motif sites
Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large...