Search Results for "markov"
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Showing 25 open source projects for "markov"
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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NMIS is a solution that provides network performance and analysis, network automation, event management and monitoring of your entire network.
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IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub repository:... -
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SnowyOwl
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... -
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. 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... -
Bravo is changing the point of sale software game for small business specialty retailers with our easy to use, all in one solution. Say goodbye to working in multiple systems. Say hello to Bravo.
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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.
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mCarts
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... -
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Muninn
A software package for estimating generalized ensemble weights in Mark
We have moved to GitHub: https://github.com/muninnorg/muninn As of July 2015 we have moved to GitHub. The SourceForge page will preserved, with the old releases. Muninn is a software package for estimating generalized ensemble weights in Markov chain Monte Carlo (MCMC) simulations. The method is full automated and makes use of the generalized multihistogram (GMH) equations for estimation the density of states [1]. The package is implemented in C++ and has a convenient interface. -
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
NOTE: TransGeneScan is migrated to Github (https://github.com/COL-IU/TransGeneScan). TransGeneScan is no longer maintained in SourceForge. Please find the latest version in Github. TransGeneScan is a gene finding tool for Metatranscriptomic sequences. TransGeneScan incorporates strand-specic hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net... -
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StatAlign
An extendable statistical multiple alignment tool.
StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single... -
Every project you pursue is a choice. With ClickTime, you’ll have the tools to track how much effort is placed into each initiative, measure their costs, and analyze their performance. So when it’s time to choose your next project, you’ll always know which ones are worth investing in.
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FamSeq
Variant calling on the basis of pedigree information
... implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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MetaDomain
Protein domain classification for short sequences
MetaDomain is a protein domain classification tool designed for very short next-generation sequencing reads. It achieves better sensitivity and low false positive rate compared with the state-of-the-art profile hidden Markov model (profile HMM) alignment tool in identifying encoded domains from short sequences. -
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MGEScan is a suite of two software tools MGEScan-LTR and MGEScan-non-LTR. MGEScan-LTR is a software that can identify new LTR retrotransposons without relying on a library of known elements. It uses approximate string matching technique and protein domain analysis to detect intact LTR retrotransposons. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons...
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Protdraw
Create portable, flexible domain drawings of protein sequences
... of hidden Markov models and formats results for ProtDraw. Highest-scoring domains are selected in cases of overlap. Domain drawings may be organized by sequence classification. -
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ConoSorter
A Large-scale Cone Snail Transcriptome/Proteome Analysis Program
ConoSorter is a high-throughput standalone program that implements regular expressions and profile Hidden Markov Models (pHMMs) for large-scale identification and classification of precursor conopeptides into gene superfamilies and classes based on the ER signal, pro-, and mature conopeptide regions generated from raw next-generation transcriptomic or proteomic data. ConoSorter also generates a set of relevant additional information (frequency of protein sequences, length, number of cysteine... -
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GenNon-h
Simulating non-homogeneous multiple sequence alignments
A number of software packages are available to generate DNA MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). GenNon-H is the first package designed to generate multiple sequence... -
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segment
Solve the Viterbi algorithm in a data stream
It is often necessary to assign a series of discrete values to continuosly variable data sequenced by time, position, etc., thereby parsing the data into fewer and larger segments of variable width. The 'segment' utility takes an input data stream as a Hidden Markov Model and applies the Viterbi algorithm to find the most likely segmentation path through the data. -
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EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.
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ESMERALDA is a development environment for statistical recognizers operating on sequential data (speech, handwriting, biological sequences). It supports continuous density Hidden Markov models, Markov chain (N-gramm) models, and Gaussian mixture models.
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RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.
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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.
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Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.
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hmm2gviz is a tool used for converting hidden Markov models generated by HMMER into a graph visualization using Graphviz.
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DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.
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HmmSDK is a hidden Markov model (HMM) software development kit written in Java. It consists of core library of HMM functions (Forward-backward, Viterbi, and Baum-Welch algorithms) and toolkits for application development.
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