[Molecular-evolution] estimating branch length - phylip

npriya via mol-evol%40net.bio.net (by npriyarao from gmail.com)
Wed Feb 21 20:38:03 EST 2007


Hi,

I am a new user of phylip. I want to scale a phylogenetic tree.

I constructed a max likelihood tree (dnaml) after using seqboot (500
bootstraps) and then performed a consense to get a final tree. The
tree looks fine but ofcourse it does not display branch lengths
(rather it displays bootstrap values).

So I took this tree, used retree to unroot and eliminate the bootstrap
values. I called this "intree". Now when I use the dnaml again with
the user tree option on the "intree" i am consistently getting an
error message which states that there is insufficient memory. I
understand that this problem is due to a badfile format but I don't
understand what could be wrong with my file.

Has anyone come across this. I would greatly appreciate any help. I
have pasted my tree file here just in case someone can spot a problem.

Is there any way to measure branch lengths?

((((((Gbremensis,Geobacbemi),Geobachumi),Trichoroba),
(Gchapellei,Ppropionic)),
(((Gmetallire,Ggrbicium),Ghydrogeno),Gsulfurred)),(((((DmonasSval,
Dsacetoxid),Dmonasthio),((((Geopsychro,Dmusaferri),
((Dmusabakii,Dmusakysin),
(DemusaspS1,Dmusasucci))),(KM,(Malonomona,(Pmasselien,Pacidigall)))),
Geothermob)),(((Dsacetexig,(Dmonasmich,Dschloroet)),
((Pvenetianu,Pacetyleni),
Pcarbinoli)),DmonasPalm)),Sedimentoc),Gpelophilu);

Thanks a ton,
Priya



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