Difference between revisions of "Phylogenetics: Python Primer"

Revision as of 20:20, 3 February 2009

	EEB 349: Phylogenetics
	This lab represents an introduction to the Python computing language, which will be useful for upcoming homework assignments as well as for software written as Python extensions (i.e. Phycas)

What is Python?

Python is one of two programming languages that we will use this semester (the other being R). One might make the case that programs like PAUP that are associated with a unique command language also represent programming languages; however, Python and R are different in being general purpose (i.e. not written specifically for phylogenetics).

Python is one of a number of different high-level computing languages in common use. All of the software we use is written in one of these languages. PAUP is written entirely in the C language, while SplitsTree is written in Java. Knowing a little bit of computer programming can save you immense amounts of time by allowing you to automate things. You will being realizing these savings doing homework for this class. While it is possible to do all the homework assignments by hand using a calculator, you will find that using Python will save you time and is more accurate (a mistake on a calculator early on in a calculation can be very costly in terms of time and accuracy). Python is a good language to learn first because it is relatively simple (not many words or punctuation rules to learn) and is much more forgiving than other languages. It is in a class of languages known as scripting languages because the program is interpreted as it is read - languages such as C require two additional steps (compiling and linking) before they can be run.

=== Installing Python ===If you have a Mac, then Python is probably already installed on your computer because it is used in many parts of the MacOSX operating system.