This is basically just a link dump, but it is to good not to put it somewhere: Hi! Meiosis
The phylogenetic tree contest
The bigger your phylogenetic tree, the bigger your headache! And I’m not just talking about the huge amount of time it will take to calculate the alignments and the actual tree using PhyloBayes or PhyML. Interpretation will become near impossible. ‘Simplify’ is the magic word here, I think, but at some point you have to look at your phylogenetic tree as a whole…
I recently teamed up with a collegue to work together on a project because our individual research projects crossed paths. We devided work and each picked a gene family to work on. The resulting phylogenetic trees are depicted below.
Sometimes you can not beat good old fashioned paper 
.
I’m using Dendroscope as my prefered tree viewer, but I don’t know if there is anything better out there for viewing large phylogenies. If somebody can recomment me something, please drop me a comment!
Muchas gracias!
I organized a small drink in the department a week ago and I asked everybody to chip in. Somehow everybody was without cash that day and offered to pay me back on Monday. Now, I’m known to like beer. Belgian beers specifically. Heck, we even went to Rochefort for our honeymoon and brought back a trunk full of the stuff. But I am digressing… Instead of money, one of the Post-Docs in the group brought me a beer instead… Westvleteren 12! Jay! Since I suspect that he has this blog marked in his Google Reader I’m posting this to see if I am correct! So here’s to you Gabino! Muchas gracias!
Fortunately my wife shares my taste for Belgian beers and we are known to grade beers. Now, Westvleteren is a very special brewery in that it is one of the seven Trappist monastery breweries. But unlike the other six Westvleteren does not sell its beer through retail. In fact, you can only buy the beer at the monastery for your own consumption. The Westvleteren 12 is rated as one of the best beers in the world, which unfortunately does not work well for the monks. Anyway, I got one and I agree with the rest of the world. It is definitely my favorite!
Apparently I need to have a Windows, a Linux AND a Mac machine
Right! Bioinformaticians are a industrious lot. Writing all kinds of software to make life easier for other scientists… But why do some write their software to work on only one OS? I know JAVA is not everything, but it works! And most scripting languages you can install and run on nearly every OS (Perl, Python, etc).
I found this article in my email and at first sight it looked nice and useful to me, but I’m not even gonna try to read the article and try the software… Because I don’t have a Mac…
Should I get a Mac?
Retrieving an unknown number of backreferences
I have been racking my brains over this, but could not find help anywhere. It seems that doing wacky stuff in Perl out of desperation actually pays off!
I wanted to search a string using this regexp without knowing how many matches I would find:
$string =~ /\(\d+):/g
This would match ’15′ and ’20′ in a string which looks like this :
$string = "(yeast:0.12313,((zebrafish:0.12312,fugu:0.84134)15:0.52313,
human:0.94424)20:0.93313);";
One can access the found values by using backreferences (in this case $1 and $2). But what if you do not know how many backreferences there are?
This piece of perl code will return the values of all the backreferences:
my @array;
while ($string =~ /\)(\d+):/g) {
push @array, $1;
}
@array will contain the values of all the backreferences. Don’t ask me why this works…
The author
My name is John van Dam and I am a Post-Doc at St. Radboud University Medical Center (NL). My research involves bioinformatics and comparative genomics on cilia and signal transduction pathways.
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