[BiO BB] Phylogeny trees on many sequences?

[Burke Squires]

Hello,

I am working on assembling phylogenic trees on multiple sets of large  
numbers of sequences, in some cases more then 3000 sequences. What is  
the best way to align these sequences and assemble a tree? I am  
interested in trees which calculate the lengths of the branches.

I have dome some multiple sequence alignment using muscle which works  
in a reasonable amount of time. However, what options are available  
for creating trees from muscle output?

Sincerely,

Burke