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Analysis of molecular variance

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Analysis of molecular variance ( AMOVA ), is a statistical model for the molecular algorithm in a single species , typically biological . The name and model are inspired by ANOVA . The method was developed by Laurent Excoffier , Peter Smouse and Joseph Quattro at Rutgers University in 1992.

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71-480: Since developing AMOVA, Excoffier has written a program for running such analyses. This program, which runs on Windows , is called Arlequin and is freely available on Excoffier's website. There are also implementations in R language in the ade4 and the pegas packages, both available on CRAN (Comprehensive R Archive Network). Another implementation is in Info-Gen , which also runs on Windows . The student version

142-509: A compiler written for the language. ( Assembly language programs are translated using an assembler .) The resulting file is called an executable . Alternatively, source code may execute within an interpreter written for the language. If the executable is requested for execution, then the operating system loads it into memory and starts a process . The central processing unit will soon switch to this process so it can fetch, decode, and then execute each machine instruction. If

213-462: A list of integers could be called integer_list . In object-oriented jargon, abstract datatypes are called classes . However, a class is only a definition; no memory is allocated. When memory is allocated to a class and bound to an identifier , it is called an object . Object-oriented imperative languages developed by combining the need for classes and the need for safe functional programming . A function, in an object-oriented language,

284-422: A programming language . Programming language features exist to provide building blocks to be combined to express programming ideals. Ideally, a programming language should: The programming style of a programming language to provide these building blocks may be categorized into programming paradigms . For example, different paradigms may differentiate: Each of these programming styles has contributed to

355-428: A store which consisted of memory to hold 1,000 numbers of 50 decimal digits each. Numbers from the store were transferred to the mill for processing. The engine was programmed using two sets of perforated cards. One set directed the operation and the other set inputted the variables. However, the thousands of cogged wheels and gears never fully worked together. Ada Lovelace worked for Charles Babbage to create

426-402: A compiler can make it crash when parsing some large source file, a simplification of the test case that results in only few lines from the original source file can be sufficient to reproduce the same crash. Trial-and-error/divide-and-conquer is needed: the programmer will try to remove some parts of the original test case and check if the problem still exists. When debugging the problem in a GUI,

497-620: A description of the Analytical Engine (1843). The description contained Note G which completely detailed a method for calculating Bernoulli numbers using the Analytical Engine. This note is recognized by some historians as the world's first computer program . In 1936, Alan Turing introduced the Universal Turing machine , a theoretical device that can model every computation. It is a finite-state machine that has an infinitely long read/write tape. The machine can move

568-540: A few simple readability transformations made code shorter and drastically reduced the time to understand it. Following a consistent programming style often helps readability. However, readability is more than just programming style. Many factors, having little or nothing to do with the ability of the computer to efficiently compile and execute the code, contribute to readability. Some of these factors include: The presentation aspects of this (such as indents, line breaks, color highlighting, and so on) are often handled by

639-584: A language's basic syntax . The syntax of the language BASIC (1964) was intentionally limited to make the language easy to learn. For example, variables are not declared before being used. Also, variables are automatically initialized to zero. Here is an example computer program, in Basic, to average a list of numbers: Once the mechanics of basic computer programming are learned, more sophisticated and powerful languages are available to build large computer systems. Improvements in software development are

710-521: A profound influence on programming language design. Emerging from a committee of European and American programming language experts, it used standard mathematical notation and had a readable, structured design. Algol was first to define its syntax using the Backus–Naur form . This led to syntax-directed compilers. It added features like: Algol's direct descendants include Pascal , Modula-2 , Ada , Delphi and Oberon on one branch. On another branch

781-470: A result, loses efficiency and the ability for low-level manipulation). Debugging is a very important task in the software development process since having defects in a program can have significant consequences for its users. Some languages are more prone to some kinds of faults because their specification does not require compilers to perform as much checking as other languages. Use of a static code analysis tool can help detect some possible problems. Normally

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852-572: A result, the computer could be programmed quickly and perform calculations at very fast speeds. Presper Eckert and John Mauchly built the ENIAC. The two engineers introduced the stored-program concept in a three-page memo dated February 1944. Later, in September 1944, John von Neumann began working on the ENIAC project. On June 30, 1945, von Neumann published the First Draft of a Report on

923-459: A visual environment. Different programming languages support different styles of programming (called programming paradigms ). The choice of language used is subject to many considerations, such as company policy, suitability to task, availability of third-party packages, or individual preference. Ideally, the programming language best suited for the task at hand will be selected. Trade-offs from this ideal involve finding enough programmers who know

994-410: Is Entity-Relationship Modeling ( ER Modeling ). Implementation techniques include imperative languages ( object-oriented or procedural ), functional languages , and logic programming languages. It is very difficult to determine what are the most popular modern programming languages. Methods of measuring programming language popularity include: counting the number of job advertisements that mention

1065-585: Is a stub . You can help Misplaced Pages by expanding it . Computer program A computer program is a sequence or set of instructions in a programming language for a computer to execute . It is one component of software , which also includes documentation and other intangible components. A computer program in its human-readable form is called source code . Source code needs another computer program to execute because computers can only execute their native machine instructions . Therefore, source code may be translated to machine instructions using

1136-418: Is assigned to a class. An assigned function is then referred to as a method , member function , or operation . Object-oriented programming is executing operations on objects . Object-oriented languages support a syntax to model subset/superset relationships. In set theory , an element of a subset inherits all the attributes contained in the superset. For example, a student is a person. Therefore,

1207-607: Is directly executed by the central processing unit . Proficient programming usually requires expertise in several different subjects, including knowledge of the application domain , details of programming languages and generic code libraries , specialized algorithms, and formal logic . Auxiliary tasks accompanying and related to programming include analyzing requirements , testing , debugging (investigating and fixing problems), implementation of build systems , and management of derived artifacts , such as programs' machine code . While these are sometimes considered programming, often

1278-571: Is free and fully functional. Native language of the application is Spanish but an English version is also available. An additional free statistical package, GenAlEx, is geared toward teaching as well as research and allows for complex genetic analyses to be employed and compared within the commonly used Microsoft Excel interface. This software allows for calculation of analyses such as AMOVA, as well as comparisons with other types of closely related statistics including F-statistics and Shannon's index, and more. This statistics -related article

1349-464: Is little more than a different notation for a machine language, two machines with different instruction sets also have different assembly languages. High-level languages made the process of developing a program simpler and more understandable, and less bound to the underlying hardware . The first compiler related tool, the A-0 System , was developed in 1952 by Grace Hopper , who also coined

1420-542: Is still strong in corporate data centers often on large mainframe computers , Fortran in engineering applications, scripting languages in Web development, and C in embedded software . Many applications use a mix of several languages in their construction and use. New languages are generally designed around the syntax of a prior language with new functionality added, (for example C++ adds object-orientation to C, and Java adds memory management and bytecode to C++, but as

1491-553: Is to alter the electrical resistivity and conductivity of a semiconductor junction . First, naturally occurring silicate minerals are converted into polysilicon rods using the Siemens process . The Czochralski process then converts the rods into a monocrystalline silicon , boule crystal . The crystal is then thinly sliced to form a wafer substrate . The planar process of photolithography then integrates unipolar transistors, capacitors , diodes , and resistors onto

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1562-434: Is usually easier to code in "high-level" languages than in "low-level" ones. Programming languages are essential for software development. They are the building blocks for all software, from the simplest applications to the most sophisticated ones. Allen Downey , in his book How To Think Like A Computer Scientist , writes: Many computer languages provide a mechanism to call functions provided by shared libraries . Provided

1633-812: The new statement. A module's other file is the source file . Here is a C++ source file for the GRADE class in a simple school application: Here is a C++ header file for the PERSON class in a simple school application: Computer programming Computer programming or coding is the composition of sequences of instructions, called programs , that computers can follow to perform tasks. It involves designing and implementing algorithms , step-by-step specifications of procedures, by writing code in one or more programming languages . Programmers typically use high-level programming languages that are more easily intelligible to humans than machine code , which

1704-624: The IBM System/360 (1964) had a CPU made from circuit boards containing discrete components on ceramic substrates . The Intel 4004 (1971) was a 4- bit microprocessor designed to run the Busicom calculator. Five months after its release, Intel released the Intel 8008 , an 8-bit microprocessor. Bill Pentz led a team at Sacramento State to build the first microcomputer using the Intel 8008:

1775-504: The Jacquard loom could produce entirely different weaves by changing the "program" – a series of pasteboard cards with holes punched in them. Code-breaking algorithms have also existed for centuries. In the 9th century, the Arab mathematician Al-Kindi described a cryptographic algorithm for deciphering encrypted code, in A Manuscript on Deciphering Cryptographic Messages . He gave

1846-485: The Sac State 8008 (1972). Its purpose was to store patient medical records. The computer supported a disk operating system to run a Memorex , 3- megabyte , hard disk drive . It had a color display and keyboard that was packaged in a single console. The disk operating system was programmed using IBM's Basic Assembly Language (BAL) . The medical records application was programmed using a BASIC interpreter. However,

1917-550: The circuits . At its core, it was a series of Pascalines wired together. Its 40 units weighed 30 tons, occupied 1,800 square feet (167 m ), and consumed $ 650 per hour ( in 1940s currency ) in electricity when idle. It had 20 base-10 accumulators . Programming the ENIAC took up to two months. Three function tables were on wheels and needed to be rolled to fixed function panels. Function tables were connected to function panels by plugging heavy black cables into plugboards . Each function table had 728 rotating knobs. Programming

1988-404: The programming environment to advance from a computer terminal (until the 1990s) to a graphical user interface (GUI) computer. Computer terminals limited programmers to a single shell running in a command-line environment . During the 1970s, full-screen source code editing became possible through a text-based user interface . Regardless of the technology available, the goal is to program in

2059-439: The source code editor , but the content aspects reflect the programmer's talent and skills. Various visual programming languages have also been developed with the intent to resolve readability concerns by adopting non-traditional approaches to code structure and display. Integrated development environments (IDEs) aim to integrate all such help. Techniques like Code refactoring can enhance readability. The academic field and

2130-568: The 9th century, a programmable music sequencer was invented by the Persian Banu Musa brothers, who described an automated mechanical flute player in the Book of Ingenious Devices . In 1206, the Arab engineer Al-Jazari invented a programmable drum machine where a musical mechanical automaton could be made to play different rhythms and drum patterns, via pegs and cams . In 1801,

2201-526: The AE in 1837. In the 1880s, Herman Hollerith invented the concept of storing data in machine-readable form. Later a control panel (plug board) added to his 1906 Type I Tabulator allowed it to be programmed for different jobs, and by the late 1940s, unit record equipment such as the IBM 602 and IBM 604 , were programmed by control panels in a similar way, as were the first electronic computers . However, with

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2272-502: The EDVAC , which equated the structures of the computer with the structures of the human brain. The design became known as the von Neumann architecture . The architecture was simultaneously deployed in the constructions of the EDVAC and EDSAC computers in 1949. The IBM System/360 (1964) was a family of computers, each having the same instruction set architecture . The Model 20 was

2343-433: The ENIAC also involved setting some of the 3,000 switches. Debugging a program took a week. It ran from 1947 until 1955 at Aberdeen Proving Ground , calculating hydrogen bomb parameters, predicting weather patterns, and producing firing tables to aim artillery guns. Instead of plugging in cords and turning switches, a stored-program computer loads its instructions into memory just like it loads its data into memory. As

2414-640: The cheaper Intel 8088 . IBM embraced the Intel 8088 when they entered the personal computer market (1981). As consumer demand for personal computers increased, so did Intel's microprocessor development. The succession of development is known as the x86 series . The x86 assembly language is a family of backward-compatible machine instructions . Machine instructions created in earlier microprocessors were retained throughout microprocessor upgrades. This enabled consumers to purchase new computers without having to purchase new application software . The major categories of instructions are: VLSI circuits enabled

2485-414: The circumstances. The first step in most formal software development processes is requirements analysis , followed by testing to determine value modeling, implementation, and failure elimination (debugging). There exist a lot of different approaches for each of those tasks. One approach popular for requirements analysis is Use Case analysis. Many programmers use forms of Agile software development where

2556-495: The code, making it easy to target varying machine instruction sets via compilation declarations and heuristics . Compilers harnessed the power of computers to make programming easier by allowing programmers to specify calculations by entering a formula using infix notation . Programs were mostly entered using punched cards or paper tape . By the late 1960s, data storage devices and computer terminals became inexpensive enough that programs could be created by typing directly into

2627-419: The computer was an evolutionary dead-end because it was extremely expensive. Also, it was built at a public university lab for a specific purpose. Nonetheless, the project contributed to the development of the Intel 8080 (1974) instruction set . In 1978, the modern software development environment began when Intel upgraded the Intel 8080 to the Intel 8086 . Intel simplified the Intel 8086 to manufacture

2698-467: The computers. Text editors were also developed that allowed changes and corrections to be made much more easily than with punched cards . Whatever the approach to development may be, the final program must satisfy some fundamental properties. The following properties are among the most important: Using automated tests and fitness functions can help to maintain some of the aforementioned attributes. In computer programming, readability refers to

2769-548: The concept of the stored-program computer introduced in 1949, both programs and data were stored and manipulated in the same way in computer memory . Machine code was the language of early programs, written in the instruction set of the particular machine, often in binary notation. Assembly languages were soon developed that let the programmer specify instructions in a text format (e.g., ADD X, TOTAL), with abbreviations for each operation code and meaningful names for specifying addresses. However, because an assembly language

2840-549: The configuration, an execute button was pressed. This process was then repeated. Computer programs also were automatically inputted via paper tape , punched cards or magnetic-tape . After the medium was loaded, the starting address was set via switches, and the execute button was pressed. A major milestone in software development was the invention of the Very Large Scale Integration (VLSI) circuit (1964). Following World War II , tube-based technology

2911-434: The descendants include C , C++ and Java . BASIC (1964) stands for "Beginner's All-Purpose Symbolic Instruction Code". It was developed at Dartmouth College for all of their students to learn. If a student did not go on to a more powerful language, the student would still remember Basic. A Basic interpreter was installed in the microcomputers manufactured in the late 1970s. As the microcomputer industry grew, so did

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2982-510: The ease with which a human reader can comprehend the purpose, control flow , and operation of source code . It affects the aspects of quality above, including portability, usability and most importantly maintainability. Readability is important because programmers spend the majority of their time reading, trying to understand, reusing, and modifying existing source code, rather than writing new source code. Unreadable code often leads to bugs, inefficiencies, and duplicated code . A study found that

3053-527: The engineering practice of computer programming are concerned with discovering and implementing the most efficient algorithms for a given class of problems. For this purpose, algorithms are classified into orders using Big O notation , which expresses resource use—such as execution time or memory consumption—in terms of the size of an input. Expert programmers are familiar with a variety of well-established algorithms and their respective complexities and use this knowledge to choose algorithms that are best suited to

3124-460: The first Fortran standard in 1966. In 1978, Fortran 77 became the standard until 1991. Fortran 90 supports: COBOL (1959) stands for "COmmon Business Oriented Language". Fortran manipulated symbols. It was soon realized that symbols did not need to be numbers, so strings were introduced. The US Department of Defense influenced COBOL's development, with Grace Hopper being a major contributor. The statements were English-like and verbose. The goal

3195-400: The first description of cryptanalysis by frequency analysis , the earliest code-breaking algorithm. The first computer program is generally dated to 1843 when mathematician Ada Lovelace published an algorithm to calculate a sequence of Bernoulli numbers , intended to be carried out by Charles Babbage 's Analytical Engine . However, Charles Babbage himself had written a program for

3266-404: The first step in debugging is to attempt to reproduce the problem. This can be a non-trivial task, for example as with parallel processes or some unusual software bugs. Also, specific user environment and usage history can make it difficult to reproduce the problem. After the bug is reproduced, the input of the program may need to be simplified to make it easier to debug. For example, when a bug in

3337-464: The functions in a library follow the appropriate run-time conventions (e.g., method of passing arguments ), then these functions may be written in any other language. Computer programmers are those who write computer software. Their jobs usually involve: Although programming has been presented in the media as a somewhat mathematical subject, some research shows that good programmers have strong skills in natural human languages, and that learning to code

3408-479: The language BCPL was replaced with B , and AT&T Bell Labs called the next version "C". Its purpose was to write the UNIX operating system . C is a relatively small language, making it easy to write compilers. Its growth mirrored the hardware growth in the 1980s. Its growth also was because it has the facilities of assembly language , but uses a high-level syntax . It added advanced features like: C allows

3479-404: The language to build a team, the availability of compilers for that language, and the efficiency with which programs written in a given language execute. Languages form an approximate spectrum from "low-level" to "high-level"; "low-level" languages are typically more machine-oriented and faster to execute, whereas "high-level" languages are more abstract and easier to use but execute less quickly. It

3550-465: The language, the number of books sold and courses teaching the language (this overestimates the importance of newer languages), and estimates of the number of existing lines of code written in the language (this underestimates the number of users of business languages such as COBOL). Some languages are very popular for particular kinds of applications, while some languages are regularly used to write many different kinds of applications. For example, COBOL

3621-400: The language. Basic pioneered the interactive session . It offered operating system commands within its environment: However, the Basic syntax was too simple for large programs. Recent dialects added structure and object-oriented extensions. Microsoft's Visual Basic is still widely used and produces a graphical user interface . C programming language (1973) got its name because

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3692-485: The matrix was to burn out the unneeded connections. There were so many connections, firmware programmers wrote a computer program on another chip to oversee the burning. The technology became known as Programmable ROM . In 1971, Intel installed the computer program onto the chip and named it the Intel 4004 microprocessor . The terms microprocessor and central processing unit (CPU) are now used interchangeably. However, CPUs predate microprocessors. For example,

3763-476: The programmer can try to skip some user interaction from the original problem description and check if the remaining actions are sufficient for bugs to appear. Scripting and breakpointing are also part of this process. Debugging is often done with IDEs . Standalone debuggers like GDB are also used, and these often provide less of a visual environment, usually using a command line . Some text editors such as Emacs allow GDB to be invoked through them, to provide

3834-443: The programmer to control which region of memory data is to be stored. Global variables and static variables require the fewest clock cycles to store. The stack is automatically used for the standard variable declarations . Heap memory is returned to a pointer variable from the malloc() function. In the 1970s, software engineers needed language support to break large projects down into modules . One obvious feature

3905-494: The result of improvements in computer hardware . At each stage in hardware's history, the task of computer programming changed dramatically. In 1837, Jacquard's loom inspired Charles Babbage to attempt to build the Analytical Engine . The names of the components of the calculating device were borrowed from the textile industry. In the textile industry, yarn was brought from the store to be milled. The device had

3976-438: The set of students is a subset of the set of persons. As a result, students inherit all the attributes common to all persons. Additionally, students have unique attributes that other people do not have. Object-oriented languages model subset/superset relationships using inheritance . Object-oriented programming became the dominant language paradigm by the late 1990s. C++ (1985) was originally called "C with Classes". It

4047-467: The smallest and least expensive. Customers could upgrade and retain the same application software . The Model 195 was the most premium. Each System/360 model featured multiprogramming —having multiple processes in memory at once. When one process was waiting for input/output , another could compute. IBM planned for each model to be programmed using PL/1 . A committee was formed that included COBOL , Fortran and ALGOL programmers. The purpose

4118-418: The source code is requested for execution, then the operating system loads the corresponding interpreter into memory and starts a process. The interpreter then loads the source code into memory to translate and execute each statement . Running the source code is slower than running an executable . Moreover, the interpreter must be installed on the computer. The "Hello, World!" program is used to illustrate

4189-430: The synthesis of different programming languages . A programming language is a set of keywords , symbols , identifiers , and rules by which programmers can communicate instructions to the computer. They follow a set of rules called a syntax . Programming languages get their basis from formal languages . The purpose of defining a solution in terms of its formal language is to generate an algorithm to solve

4260-447: The tape back and forth, changing its contents as it performs an algorithm . The machine starts in the initial state, goes through a sequence of steps, and halts when it encounters the halt state. All present-day computers are Turing complete . The Electronic Numerical Integrator And Computer (ENIAC) was built between July 1943 and Fall 1945. It was a Turing complete , general-purpose computer that used 17,468 vacuum tubes to create

4331-411: The term software development is used for this larger overall process – with the terms programming , implementation , and coding reserved for the writing and editing of code per se. Sometimes software development is known as software engineering , especially when it employs formal methods or follows an engineering design process . Programmable devices have existed for centuries. As early as

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4402-409: The term 'compiler'. FORTRAN , the first widely used high-level language to have a functional implementation, came out in 1957, and many other languages were soon developed—in particular, COBOL aimed at commercial data processing, and Lisp for computer research. These compiled languages allow the programmer to write programs in terms that are syntactically richer, and more capable of abstracting

4473-561: The underlining problem. An algorithm is a sequence of simple instructions that solve a problem. The evolution of programming languages began when the EDSAC (1949) used the first stored computer program in its von Neumann architecture . Programming the EDSAC was in the first generation of programming language . Imperative languages specify a sequential algorithm using declarations , expressions , and statements : FORTRAN (1958)

4544-560: The various stages of formal software development are more integrated together into short cycles that take a few weeks rather than years. There are many approaches to the Software development process. Popular modeling techniques include Object-Oriented Analysis and Design ( OOAD ) and Model-Driven Architecture ( MDA ). The Unified Modeling Language ( UML ) is a notation used for both the OOAD and MDA. A similar technique used for database design

4615-448: The wafer to build a matrix of metal–oxide–semiconductor (MOS) transistors. The MOS transistor is the primary component in integrated circuit chips . Originally, integrated circuit chips had their function set during manufacturing. During the 1960s, controlling the electrical flow migrated to programming a matrix of read-only memory (ROM). The matrix resembled a two-dimensional array of fuses. The process to embed instructions onto

4686-427: Was designed to expand C's capabilities by adding the object-oriented facilities of the language Simula . An object-oriented module is composed of two files. The definitions file is called the header file . Here is a C++ header file for the GRADE class in a simple school application: A constructor operation is a function with the same name as the class name. It is executed when the calling operation executes

4757-436: Was replaced with point-contact transistors (1947) and bipolar junction transistors (late 1950s) mounted on a circuit board . During the 1960s , the aerospace industry replaced the circuit board with an integrated circuit chip . Robert Noyce , co-founder of Fairchild Semiconductor (1957) and Intel (1968), achieved a technological improvement to refine the production of field-effect transistors (1963). The goal

4828-405: Was to decompose large projects physically into separate files . A less obvious feature was to decompose large projects logically into abstract data types . At the time, languages supported concrete (scalar) datatypes like integer numbers, floating-point numbers, and strings of characters . Abstract datatypes are structures of concrete datatypes, with a new name assigned. For example,

4899-433: Was to design a language so managers could read the programs. However, the lack of structured statements hindered this goal. COBOL's development was tightly controlled, so dialects did not emerge to require ANSI standards. As a consequence, it was not changed for 15 years until 1974. The 1990s version did make consequential changes, like object-oriented programming . ALGOL (1960) stands for "ALGOrithmic Language". It had

4970-425: Was to develop a language that was comprehensive, easy to use, extendible, and would replace Cobol and Fortran. The result was a large and complex language that took a long time to compile . Computers manufactured until the 1970s had front-panel switches for manual programming. The computer program was written on paper for reference. An instruction was represented by a configuration of on/off settings. After setting

5041-423: Was unveiled as "The IBM Mathematical FORmula TRANslating system". It was designed for scientific calculations, without string handling facilities. Along with declarations , expressions , and statements , it supported: It succeeded because: However, non-IBM vendors also wrote Fortran compilers, but with a syntax that would likely fail IBM's compiler. The American National Standards Institute (ANSI) developed

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