Mac

Mac OS X Hints & Tips

	MacOS X Bioinformatics & Molecular Evolution tools
		MacOS X software ClustalX2: a graphic multiple alignment program [ftp://ftp.ebi.ac.uk/pub/software/clustalw2/] SeaView: a multiple alignment editor with Clustalw and Muscle [http://pbil.univ-lyon1.fr/software/seaview.html/] Se-Al v2.0a11 Carbon: Sequence Alignment Editor [http://tree.bio.ed.ac.uk/software/seal/] FigTree: a graphic viewer of phylogenetic trees [http://tree.bio.ed.ac.uk/software/figtree/] TreeDyn: Towards dynamic graphics and annotations for analyses of trees [http://www.treedyn.org/] TreeView X: a phylogenetic tree viewer (this version has still some limitations) [http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/] Seq-Gen: a sequence simulator [http://tree.bio.ed.ac.uk/software/seqgen/] Sequence Analysis for Mac OS X by William A. Gilbert [http://informagen.com/SA/] MacVector a molecular biology and bioinformatics software [http://www.macvector.com/] VectorNTI: free for academia, but only up to OS 10.3 (Panther) [http://www.invitrogen.com/content.cfm?pageid=10130] *PAUP 4.0: A tool for phylogenetic analysis (Classic OS only, Unix version without GUI available for OS X) [http://paup.csit.fsu.edu/index.html] MacClade 4.05**: a tool for phylogenetic analysis [http://macclade.org/macclade.html]
		Unix command-line sofware (There are many more than listed here. Recompliation may be required.) PHYLIP: the PHYLogeny Inference Package [http://evolution.genetics.washington.edu/phylip.html] PAML: Phylogenetic Analysis by Maximum Likelihood [http://abacus.gene.ucl.ac.uk/software/paml.html] ClustalW: a multiple seqeunce alignment program [ftp://ftp.ebi.ac.uk/pub/software/clustalw2/] EMBOSS: The European Molecular Biology Open Software Suite [http://emboss.sourceforge.net/] CodonW: Correspondence Analysis of Codon Usage [http://codonw.sourceforge.net/] GCUA: General Codon Usage Analysis [http://bioinf.may.ie/gcua/index.html] HMMER 2.3.2: biological sequence analysis using profile hidden Markov models [http://hmmer.janelia.org/] T-COFFEE: Multiple Sequence Alignment Combination [http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html]

	MacOS X utilities
		R (GNU S): A language and environment for statistical computing and graphics [http://www.r-project.org/index.html]
		MySQL: The world's most popular open source database [http://dev.mysql.com/downloads/]
		CocoaMySQL: The open source MySQL database manager for Mac OS X [http://cocoamysql.sourceforge.net/]
		Fetch: an easy-to-use, full-featured FTP and SFTP client for Apple Macintosh (free educational license) [http://www.fetchsoftworks.com/]
		Fugu: A free Mac OS X SFTP, SCP and SSH Frontend [http://rsug.itd.umich.edu/software/fugu/]
		MacSFTP Carbon: A Secure FTP application for Mac OS X [http://pro.wanadoo.fr/chombier/MacSFTP/SFTP_info.html]
		AlmostVPN: an SSH tunnel manager for Mac OS X (becomes as Preference Panel) [http://www.leapingbytes.com/almostvpn]
		Vine server: Free, fast VNC server (formerly OSXvnc) [http://www.redstonesoftware.com/products/vine/server/vineosx/index.html]
		Vine viewer: VNC viewer for OSXvnc (feature-rich, but not free) [http://www.redstonesoftware.com/products/vine/viewer/index.html]
		Chicken of the VNC: VNC client for Mac OS X [http://sourceforge.net/projects/cotvnc/]
		JollyFastVNC: Very fast VNC viewer [http://www.jinx.de/JollysFastVNC.html]
		Firefox 2: An open-source web browser [http://en.www.mozilla.com/en/]
		BBEdit: Professional HTML and text editor (TextWrangler is the free version) [http://www.barebones.com/index.html]
		GraphicConverter: A shareware for converting many picture formats and for picture manipulation [http://www.lemkesoft.com/us_gcabout.html]
		MacGhostView: A postscript viewer based on ghostscript, includes also macps2pdf (a shareware) [http://www.kiffe.com/macghostview.html]
		PCalc: A fully featured scientific calculator (a shareware) [http://www.pcalc.com/]
		ChronoSync: file and folder synchronizations and backups [http://www.econtechnologies.com/site/Pages/ChronoSync/chrono_overview.html]
		Carbon Copy Cloner: A cloning (backup) utility for Mac OS X (free for Education) [http://software.bombich.com/ccc.html]
		DiakWarrior: Essential Mac Disk Utility (commercial, but cannot live without) [http://www.alsoft.com/index.html]
	MacOS X hints & tips
	From O'Reilly MacDevCenter.com: (list of all articles) Top Ten Mac OS X Tips for Unix Geeks (05/15/2007) What Is Vim (It's Easier than You Think) (07/11/2006) Xcode for the Rest of Us, Part II (05/02/2006) Xcode for the Rest of Us (02/07/2006) Build Your Own Apache Server with mod_perl (11/05/2002) Configuring sendmail on Jaguar (09/10/2002) Setting up a Site Server with Jaguar (08/24/2002) Using IMAP on Mac OS X (05/21/2002) Learning the Mac OS X Terminal (12/14/2001 - 07/02/2002) Apache Web-Serving with Mac OS X (12/07/2001 - 04/23/2002) Secure Mail Reading on Mac OS X (03/19/2002) OSXFAQ: Tutorials (Mac OS X Unix Tutorial, and lots more!) [http://www.osxfaq.com/Tutorials/] Magical Macintosh Key Sequences [Lots of keyboard shortcuts!] How to enable WebDAV with Apache web server and publish your iCal calendar How to use PHP iCalender to view iCal calenders from any browser PHP iCalender [http://phpicalendar.sourceforge.net/] Command-Shift-4... Not your fathers screen shot any more!! Dr. Mac - Speed up Word Instantly phpMyAdmin - Administrate MySQL over the WWW. [http://www.phpmyadmin.net/] Webmonkey PHP/MySQL Tutorial
	MacOS X related links
	SecureMac.com: A site devoted to Apple Macintosh security and Mac OS X Security — http://www.securemac.com/index.php Mac OS X Hints: Get the most from X! — http://www.macosxhints.com/ Apple: Internet Developer (including HTML, CSS, Java, PHP, MySQL, and more) — http://developer.apple.com/internet/index.html Apple: Discussions — http://discussions.info.apple.com/ OSXFAQ: Technical News and Support for Mac OS X — http://www.osxfaq.com/index.ws OSXFAQ: Forum — http://forums.osxfaq.com/index.php MacFixIt: Troubleshooting solutions for the Macintosh — http://www.macfixit.com/ MacNN: The Macintosh News Network — http://www.macnn.com/ MacWorld; http://www.macworld.com/ MacRumors.com — http://www.macrumors.com/ AppleInsider — http://www.appleinsider.com/ MacTech Magazine — http://www.mactech.com/ O'Reilly Network - Mac DevCenter — http://www.oreillynet.com/mac/ Fink: Unix Open Source software for Darwin/Mac OS X — http://www.finkproject.org/index.php Marc Liyanage's Mac OS X page (including PHP, MySQL, and lots more!) — http://www.entropy.ch/software/macosx/ PHPmac.com — http://www.phpmac.com/

Mac OS X Hints & Tips

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