Question: What type of tree do phylogenetic trees use?
0
gravatar for n00514450
4.5 years ago by
n0051445020
United States
n0051445020 wrote:

I'm starting a Masters program in Bioinformatics in January and I want to prepare tools that I can use for coursework. Is it a Binary Search Tree? What information should each node store? Is it supposed to be balanced?

Is there anything else that I should prepare before I begin?

Thanks.

trees tree phylogenetic • 1.3k views
ADD COMMENTlink modified 4.5 years ago by Dan Gaston7.1k • written 4.5 years ago by n0051445020

uh ? Binary Search Tree is an algorithm, a phylogenetic tree  is a diagram.

ADD REPLYlink written 4.5 years ago by Pierre Lindenbaum119k

Is there a reason you are particularly asking about trees? IMHO you should be looking into requisite skills and languages in Bioinformatics. Focusing on one data structure/representation model makes sense only if you're planning on bettering it. From your question, it does not seem like you are planning on that.

ADD REPLYlink written 4.5 years ago by RamRS21k
1
gravatar for onuralp
4.5 years ago by
onuralp180
Turkey
onuralp180 wrote:

Here is a good talk by Joe Felsenstein to get you up to speed: Computational aspects of biological information: Reconstructing phylogenies: how? how well? why?

Good luck with the program! 

 

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by onuralp180

Thank you! This was very helpful and I realize that I'm currently way in over my head. I'll wait a little bit.

ADD REPLYlink written 4.5 years ago by n0051445020
1
gravatar for Dan Gaston
4.5 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

Echoing comments and other answers a phylogenetic tree isn't a particular data structure, beyond being an acyclic graph (in its simplest state). Depending on what you want to DO there are many different sorts of data structures you can use to represent phylogenetic trees in order to efficiently perform computations over the tree, but that is very specific for what type of research you want to do, or the question you want to ask. 

ADD COMMENTlink written 4.5 years ago by Dan Gaston7.1k

Thank you. I need to read way more before I attempt something like this. The reason is, I'll have to create a tree-building program.

ADD REPLYlink written 4.5 years ago by n0051445020

Do you NEED to create a tree building program? I mean, of course if your project is to try and make a better phylogeny program than yeah, you have to. Or if you need it to do something that none of the current programs do, then yeah. Otherwise there are a bunch of really good well developed phylogeny reconstruction programs out there. RAxML, FastTree, etc.

ADD REPLYlink written 4.5 years ago by Dan Gaston7.1k
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