Search Results for "linux basic programming"

This program implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.

set of classes used to handle input/outputs of bioinformatics data files and basic operations as multiple alignment and phylogenetic reconstruction.

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.

Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic networks among microbial communities. To infer the structure of community-level metabolic...

GaloisExplorer provides a user-friendly interface for basic functionalities of Formal Concept Analysis (FCA) with different lattice generation algorithms and an interactive viewer to explore a 3-dimensionally laid out lattice.

This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of...

The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!

Batman-Seq: Basic Alignment Tool for MAny Nucleotides. A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.

Protein Mass Spectrometry: cprobid is a software for identification peptides from MS/MS spectra. The output of this program is compartable with TransProteomic Pipeline software package (sashimi project).

Genetic programming environment to inference context free grammars base on positive and negative examples of language.

This collection of tools written in C++ with the STL library provides the basic building blocks to develop complex analysis pipelines on genomic coordinates.