[Molecular-evolution] Re: estimating branch length - phylip

Mary K. Kuhner via mol-evol%40net.bio.net (by mkkuhner from kingman.gs.washington.edu)
Thu Feb 22 15:33:19 EST 2007


In article <mailman.59.1172114161.5139.mol-evol from net.bio.net>,
npriya <npriyarao from gmail.com> wrote:

>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.

The user tree analysis needs both an intree and an infile containing
the original sequence data.  A very common error in Phylip is to
have the wrong stuff in your infile--perhaps something left over
from seqboot?

The procedure you describe should work, so I suspect you have, as you
say, a file problem--but I think it's likely in infile, not intree.
Your tree looks okay to me.

Mary Kuhner mkkuhner from u.washington.edu



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