Gourt > Science > Biology > Taxonomy > Software (4)
Computer software (or simply software) is the programs and procedures that enable a computer to perform a specific task, as opposed to the physical components of the system (hardware). This includes application software such as a word processor, which enables a user to perform a task, and system software such as an operating system, which enables other software to run properly, by interfacing with hardware and with other software.
The term "software" was first used in this sense by John W. Tukey in 1957. In computer science and software engineering, computer software is all information processed by computer systems, programs and data. The concept of reading different sequences of instructions into the memory of a device to control computations was invented by Charles Babbage as part of his difference engine. The theory that is the basis for most modern software was first proposed by Alan Turing in his 1935 essay Computable numbers with an application to the Entscheidungsproblem. Hally, Mike (2005:79). Electronic brains/Stories from the dawn of the computer age. British Broadcasting Corporation and Granta Books, London. ISBN 1-86-207663-4.
Relationship to hardware
Computer software is so called in contrast to computer hardware, which encompasses the physical interconnections and devices required to store and execute (or run) the software. In computers, software is loaded into RAM and executed in the central processing unit. At the lowest level, software consists of a machine language specific to an individual processor. A machine language consists of groups of binary values signifying processor instructions (object code), which change the state of the computer from its preceding state. Software is an ordered sequence of instructions for changing the state of the computer hardware in a particular sequence. It is generally written in high-level programming languages that are easier and more efficient for humans to use (closer to natural language) than machine language. High-level languages are compiled or interpreted into machine language object code. Software may also be written in an assembly language, essentially, a mnemonic representation of a machine language using a natural language alphabet. Assembly language must be assembled into object code via an assembler. More on [ Computer software ]
Software :: Evolution
Software :: Biology
Software :: Products and Services
Software :: Statistics
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PAUP* - PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to use, particularly the Mac version.
PHYLIP - Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range of different types of data, and runs on most platforms.
Meta Description: [ PHYLIP Phylogeny Inference Package computer
programs for inferring phylogenies ]
3I - Internet-accessible Interactive Identification - Program to create internet-accessible interactive taxonomic keys.
Component - For analysis of phlyogenies. Includes a wide range of randomisation methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available only for Windows machines, but still has some unique features. Much of the functionality is now replaced by RadCon, GeneTree, TreeMap and the latest release of PAUP.
GeneTree - Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of papers describing the methods are available from the GeneTree web page. Available for Macintosh and Windows.
MacClade - A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for entering and editing data and phylogenies and producing attractive tree diagrams and charts.
Mesquite - Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
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MrBayes - Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
Nona - A Quick Guide to the Commands - A brief overview of using Nona for phylogenetic analysis.
PAML - Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Phylo-Win - Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
Phylodendron - Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform.
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RadCon - A package implementing a wide range of consensus methods, including reduced consensus, and for calculation of MRP supertrees. Currently only available for Macs.
SuperTree - Implements various supertree building methods. Available in Linux/Unix and PC versions.
Tree Puzzle - Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
TreeMap - Experimental program for comparing host and parasite trees.
TreeView - Simple program for displaying phylogenies.
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