Search Results for "graph"

Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach.

This application allows observing genome rearrangements in prokaryotic genomes. It provides rearrangements frequencies profiles and genomes graph representation.

xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level.

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length. Please note that Mix has moved to: https://github.com/massyah/MIX

Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file.

A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.

Python library to convert networks from/to many different formats, like the ones used in Pajek, Cytoscape and other popular graph formats like GML. It also includes support to integrate experimental data to the netowork.

A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.

Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.