Reformat codes:
Click menu Source => Format
Hotkeys
Contrl + Space: suggest complete names, left click to fulfill it
Mount command
## mount read-writable disks
mount -t ext3 -o rw /dev/hdb1 /disk2
SVN quick reference
Update a file
svn commit -m “Modified version of aa.pl ” aa.pl
List content
svn ls svn://beast/Ortholog/trunk
Make new folder
svn mkdir svn://beast/Ortholog/trunk/hvs
Import all files in a folder to svn
svn import myfolder svn://comet/Ortholog/trunk/hvs
Import a file to svn
svn import bsub.pl svn://comet//Patents/trunk/tools/bsub.pl
More at
http://www.digilife.be/quickreferences/QRC/Subversion%20Quick%20Reference%20Card.pdf
Phylogenetic algorithm selection
See http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf for details, in brief:
• Continuous characters, lots of data, few computing resources ==> Neighbor joining
• Discrete characters, few mutations / homoplasy ==> Maximum Parsimony
• Discrete characters, limited sequence lengths, some homoplasy ==> Maximum Likelihood Estimation
• Discrete characters, many taxa ==> Supertree
• Complete genomes ==> Whole genome phylogeny
PID in Perl
current PID: $$
parent PID: getppid()