Search Results for "python 3"

polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences

Theodore is a tool for semi-automated hybrid assembly of genomes, improving assembly quality by combining multiple information sources.

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated...

The package enables detection of sequence variation between metagenomic samples.

Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats.

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...

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

A python/C++ framework for Bayesian phylogenetic analysis.

An open source implementation of a protein threading program based on the energy functions and techniques originally introduced by Prospect.

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

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.

DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.

trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment. trimAl implements a series of...