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Cyanobacterial phylogeny


CyanoPhy in a virtual machine

Looking for cyanobacterial phylogenetic trees? Visit cyanophylogeny.scienceontheweb.net/


INTRODUCTION

This page describes CyanoPhy, a Linux virtual hard disk for a Virtual Machine that runs under MS Windows and Mac OS. CyanoPhy is primarily intended for the study of cyanobacterial phylogeny, but may also be used for the many other purposes expected for a good OS.

If you wish to perform phylogenetic studies using the many Linux-specific programmes that are currently available, but do not have access to a Linux machine, or have never used the Linux OS but would like to try it, then please read the following.

Virtualization provides the ability to run one or more different operating systems (the guest OS) as a Virtual Machine within an existing system (the host OS).

A Virtual Machine consists of a virtual hard drive and several other files, controlled by a virtualization programme that runs directly on the host like any other programme. A Virtual Machine is simple to install and avoids the need to partition the hard disk for a new OS and the consequent use of a dual-boot process. A Virtual Machine can be employed as a full OS for working purposes, or for testing additional operating systems that are otherwise not available on the host computer. We can thus run a Linux or licensed Mac OS (or both) as guests under Windows, or a licensed Windows OS under Linux or Mac, etc. A Virtual Machine has two major advantages over a native installation: (1) the host and guest, with their OS-specific programmes, may be run simultaneously on a single computer; (2) any changes that destroy the correct functioning of the guest OS may be overcome by simply reverting to a backup copy, avoiding the need to reformat the hard disk and reinstall the OS. The latter problem may be encountered even by the most experienced user!

These advantages may particularly interest confirmed Linux users, but the system is also ideal for those who have little or no Linux experience and wish to try this wonderful OS within their familiar workspace. The Linux OS provided is heavily oriented towards studies of cyanobacterial phylogeny and gives both novice and confirmed phylogeneticists the opportunity to explore this fascinating field. Note also that the programmes will run much more rapidly on your own computer than on the multiple-user Unix servers of your Institution where you are limited by available cpu time.

 DESCRIPTION

The virtual hard drive, in Virtual Disk Image (.vdi) format, for use only on 64-bit architectures, is currently CyanoPhy.vdi and contains a completely functional version of a LINUX operating system. The recommended virtualization programme is Oracle VirtualBox. The Virtual Machine runs as a guest on Windows, Mac or Linux host systems in exactly the same way as a native Linux distribution behaves. Interaction between host and guest gives full functionality to the latter, including Internet connection and access to USB and CD/DVD devices, and files or portions of text may be transferred between the two OS in either direction.

The Linux distribution, openSUSE (currently version 14.1), has a user-friendly graphical interface and  is easily maintained by automatic updates. Existing users will note this change in OS: successive versions of Ubuntu were becoming progressively "bloated" and slow to load. The strong points for studies of cyanobacterial phylogeny are the extensive databases of aligned cyanobacterial 16S (over 6000) and 23S (over 500) rRNA sequences (maintained in the software package ARB), together with many of the Linux phylogeny programmes required for sequence manipulation and tree inference (including minimum evolution, maximum likelihood and Bayesian methods, splits graphs, PCA analysis), tree visualization, and a useful collection of shell scripts as programme aids. A full list is given in phylo-lst.pdf, and full documentation for the programmes is included. Other programmes can easily be added if required by the user.

In the Linux tradition, the operating system and installed programmes are free, and re-distribution to your colleages is both permitted and encouraged.

 THE HOST COMPUTER

The hard drive runs in the virtualization programme VirtualBox, maintained by Oracle. Versions of this freeware programme are available for Windows (XP, Vista, 7), Mac (Leopard, Snow Leopard, Lion) and Linux (most distributions) hosts, on 32- and 64-bit architectures, and must be installed to create a Virtual Machine.

A full list of supported host OS (Windows, Mac and Linux versions) may be found at https://www.virtualbox.org/manual/ch01.html#idp12689168

The Linux system is a dynamically-expanding virtual hard drive that occupies, on the physical drive, only the minimum space required by the OS and the files created by the user. This is currently about 10 GB, and will increase to a preset maximum of 50 GB as files are added. This size may be changed by the user.

 DOWNLOADS

Please see the Home page for download details.

Page last updated: 02.04.2017 by Michael Herdman

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