Open Source Bio-Computing Environments

Category	Name	What it does
Operating Systems	GNU/Linux	Gnu is Not Unix
	Mac OS X	Unix-based Apple OS
Bio Packages	NCBI BLAST	Sequence similarity search
	CLUSTALW	Multiple alignment
	PHYLIP	Phylogenetic applications
Statistical Package	R	Statistics & graphing
Database System	PostgreSQL	Relational DB
Programming Tools	Emacs	Script/Text editor
	Xemacs	X version of Emacs
	Perl	Scripting language
	Bioperl	Perl library for bio-applications
Generic Applications	Mozilla	Web browser
	Open Office	Word processing and more
	Gqview	Image viewer
	Gimp	Image editor
	gv	Postscript viewer
	xpdf	PDF viewer
UNIX Basic Tools	ls	list
	cat	concatenate
	mv	rename files
	cp	copy files
	rm	remove files (danger!!)
	more/less/head/tail	pagers
	mkdir/rmdir	make/remove directories
	cd	change directory
UNIX Power Tools	grep	pattern searching
	sed	pattern substitution
	sort	sort lines
	cut	fetch columns
	tr	character translation
	wc	word count
	ssh/scp	remote login/remote copy
	ftp/lftp	file transfer