tree construction

Mar 21, 2012 at 6:07 AM

For all......

Greetings all..

i would like to know is there is a way to construct a phylogenetic Tree for DNA or Protein Samples

thank you....

Mar 21, 2012 at 1:49 PM

I have never used in my own projects, but yes you can create Phylogenetic tree easily using .NET Bio. You need to have the file format according to the Newick notation flat file specification. 

http://evolution.genetics.washington.edu/phylip/newicktree.html
http://en.wikipedia.org/wiki/Newick_format

NewickParsernp = new NewickParser();
np.Parse(fileName);

The parse method is overloaded and it can either be a file or string or a textreader object. More details are provided in the documentation guide (chm file) under Bio.IO.Newick namespace.

Good Luck!

Mar 21, 2012 at 3:46 PM

Hi!

is it possible to automatically generate a graphic (png, bitmap, whatever...) from the Bio.Phylogenetics.Tree?
Can someone please point me to an example?

Thanks for your time and effort!
best regards,

Jan

Coordinator
Mar 21, 2012 at 6:24 PM

Not built in, no.  But this might be a fun exercise to play with -- I have a training venue at Cornell this week where we could do this with .NET Bio.  I don't have any Newick files handy - do you have one with real data, or at lest semi-real data you could share with me?  I could share the program back to you :-)

mark

Mar 21, 2012 at 11:31 PM

Thank you Mark for your positive reply.

A complex example of a Newick formated tree can be found here: http://phylogram.org/

(Edentata:55, (((Orycteropus:12, Trichechus:43):1, (Procavia:29, (Elephas:18, Loxodonta:5):55):10):15, (((Chiroptera:27, (Tupaia:43, ((Talpa:24, (Suncus:24, Erinaceus:58):6):4, (Manis:5, ((Felis:13, Leo:7):32, ((Canis:37, Ursidae:12):4, ((Phocidae:19, Zalophus:17):7, (Procyonidae:12, Mustelidae:22):9):5):17):13):3):10):6):8, (((Lemuridae:46, (Galago:16, Nycticebus:27):10):8, (Tarsius:15, ((Cebus:10, (Atelinae:5, (Aotus:6, Callithrix:9):3):3):18, ((Hylobates:6, (Pongo:1, (Gorilla:2, (Homo:22, Pan:1):2):6):2):5, (Presbytis:1, (Cercopithecus:1, (Erythrocebus:0, ('Macaca fascicularis':2, ('Macaca mulatta':5, 'Macaca fuscata':0):1, (Theropithecus:2, Papio:4):15):2):1):8):6):9):22):10):13, ((Ochotona:7, Oryctolagus:54):4, (Caviomorpha:107, (Spermophilus:29, (Spalax:23, ((Rattus:71, Mus:19):15, (Ondatra:27, Mesocricetus:32):27):20):8):12):15):11):9):12, ((Sus:50, ((Lama:10, Camelus:24):31, (Hippopotamus:31, (((Ovis:9, Capra:8):19, ((Antilocapra:13, Giraffa:14):7, (Cervus:8, Alces:9):11):2):9, (Tragelaphinae:6, ('Bos grunniens':6, (Bison:5, 'Bos taurus':15):7):11):6):47):10):19):18, ((('Equus (Asinus)':6, 'Equus caballus':31):24, (Tapirus:19, Rhinocerotidae:23):11):22, ((Phocoena:4, Tursiops:17):5, (Balaenoptera:36, Eschrichtius:2):8):29):12):12):16):55); 

However, I need to reconsider what I really want to do with it. By way of introduction I am working with metabolomics data (GC/MS) and want to visualize metabolite profiles in a Silverlight app. To annotate the experiments, we develop the XEML framework (see http://xeml.codeplex.com/ ). The output of this framework is a tree encoded in xml. Although the XEML tree is not a phylogenetic tree, I thought I could develop a XEML parser for Bio .Net and then use the Bio.Phylogenetics.Tree to render a picture of the experiment design. I thought this would be easier and straighter forward than to use the classes from the XEML framework. I need to discuss this with our developers.

Nevertheless, thank you for your offer!
best wishes,
Jan