Arb Installation on Linux

After four days of computer hassle, I finally managed to install ARB on both a Mac and a PC in under an hour!

The Mac installation was relatively easy–I followed the detailed online instructions from Mike Dyall-Smith (http://greengenes.lbl.gov/mlds/).  The Fink FAQ was also very helpful and helped solve a few command line issues.  Note:  Even though the Dyall-Smith says that you have to launch ARB in the X11 terminal, this is NOT the case on the mac in 610B–you have to launch arb in the mac terminal.

To install ARB on my desktop PC in 610B, I first installed Ubuntu inside windows (middle option on ubuntu installation window–this leaves you the option to delete ubuntu through add/remove programs if needed).  I then downloaded the ARB files for linux, and ran the installation script–much trial and error led to my discovery that most files you need to run ARB are actually included with the linux download.  The following programs I had to install additionally after getting errors while launching/running ARB itself:

  • Error while opening ARB: ‘Cannot open lib.Xm.so.3’  (To fix: sudo apt-get install lib motif3)
  • Error while trying to view alignment window: ‘Cannot open libglut.so.3’ (To fix: sudo apt-get install libglut3 [this also installs freeglut3 in the process])
  • Error while trying to view alignment window: ‘Cannot open libpng.so.3’ (To fix: sudo apt-get install lipng3)

Today I edited the following genera (Bold genera names mean I search and queried all sequences with that genera name. [Bracket] genera names mean these genera were edited alongside Bold genera as reference sequences–thus, not all sequences with this genera assignment have been searched and edited):

  • Diplolaimelloides
  • Halalaimus
  • [Trichura, Trichinella] (edited as reference to Halalaimus)
  • Anoplostoma
  • [Oncholaimidae (check22)]
  • Rhabdolaimus–edited whilst in Hull (14 May) but tree not rebuilt since this edit

Neighbour-joining tree was rebuilt overnight following edits

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