Although biologists since the time of Darwin have convincingly inferred the existence of natural selection from the current species distributions of animals and plants, and their genetic relationships, this evidence is almost always indirect and observational. By contrast, virologists have access to the remarkable field of experimental evolution, such that adaptive processes that may occur over centuries or millennia in larger organisms can be observed in viruses over days or weeks
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
https://doi.org/10.1093/molbev/mss075
Molecular Biology and Evolution, Volume 29, Issue 8, August 2012, Pages 1969–1973, Published: 25 February 2012
Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
Google Code Archive
Welcome! The Google Code Archive contains the data found on the Google Code Project Hosting Service, which will be turned down in early 2016.
This archive contains over 1.4 million projects, 1.5 million downloads, and 12.6 million issues. You can learn more about the data served from Google Cloud Storage here.
Google Code offered open-source project hosting on other domains besides just code.google.com, too. Explore the projects Google Code hosted below:
Eclipse Labs is a community of open source projects that build technology based on the Eclipse platform.
To learn more, see: http://www.eclipse.org/org/
https://web.archive.org/web/20160501221418/https://code.google.com/archive/
Google Code was launched in 2006, with the goal of making it easier to collaborate with others on open-source software. It offered Subversion, Mercurial, and Git source code hosting. It soon expanded to offer wikis, downloads, and even issue tracking.
But alas, in 2015 Google bid farewell to the service, which had since been eclipsed by other, richer open-source project hosting providers.
The Google Code Archive hosts the public project data that was housed on code.google.com and related domains. While it only provides a read-only view of projects, it should be sufficient to resurrect an open-source project that didn’t migrate elsewhere.
Schema
The Google Code Archive’s data is hosted on Google Cloud Storage. Data is retrieved using the JSON API. Documentation for the Google Code Archive data can be found here.
Redirecting Projects
If you are an administrator of a Google Code project and wish to put a URL redirect in place to its new home on the internet, please contact google-code-shutdown@google.com. Be sure to include the name of the Google Code project and the URL to redirect to.
Deleting Projects
If you are an administrator of a Google Code project and wish to delete it from the archive, please contact google-code-shutdown@google.com.
If you are not the administrator of a project and wish to remove it from the archive, for example to issue a lawful DMCA request, please use this form. When prompted for which Google product the request relates to, select „Other Projects“ and then „Code“.
ProjectSourceIssuesWikisDownloads
beast-mcmc
BEAST, a program for Bayesian analysis via MCMC of Evolution & Phylogenetics using Molecular Sequences
BEAST development has moved to GitHub. Write-access is no longer available here and wiki pages will also be moved shortly. – April 25, 2015
BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. The program is orientated towards (strict and relaxed) molecular clock analyses. It can be used as a method of constructing phylogenies, but it is also intended for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It uses an XML input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.
Download BEAST
Download BEAST v1.8.1 binaries for Mac, Windows and UNIX/Linux
Other Downloads
Documentation
YourKit is kindly supporting open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications. Take a look at YourKit’s leading software products YourKit Java Profiler and YourKit .NET Profiler.
Project Information
- License: GNU Lesser GPL
- 58 stars
- svn-based source control
Labels:
java MCMC molecular evolution bioinformatics phylogenysequence bayesian phylogenetics beast coalescent
JULIMINATION 
Hinterlasse einen Kommentar