phylogeny programs

[Hans Sluiman]

"Mary K. Kuhner" wrote:
> 
> In article <9l9hj2$qid$1 at mercury.hgmp.mrc.ac.uk>,  <rodgers at onramp.net> wrote:
> >I'm interested in "succint" comparison/critique of the various
> >algorithms/programs available for phylogenetic-type sequence analyses.
> >I understand this may be like asking for a "succint" critique of
> >Mozart, but still...
> 
> A useful web site is the course site for the Molecular Evolution
> workshop at Woods Hole:
> 
> http://courses.mbl.edu/Courses/mole.html
> 
> This contains lecture notes from a two-week intensive workshop
> on topics like this one, many of which have very good reference
> lists.  For your particular questions, try the lecture by Joseph
> Felsenstein on bootstraps and other means of assessing tree
> reliabilities, and the lecture by Paul Lewis on comparing different
> phylogeny methods.
> 
> >    In particular - is there a way to assess the "error" or confidence
> >level in a tree?  I understand there are some outputs that indicate
> >the percentage of bootstrap trees that give the final tree shape.
> 
> The program package PHYLIP  and the program PAUP* can both
> carry out a bootstrap analysis, and have good documentation on
> how the method works.  Have a look at their web pages.  PHYLIP
> is free; PAUP* has more features and a slicker interface; both are
> pretty reliable.
> 
> Different tree estimation methods also come with their own
> internal tree-support measures.  For example, likelihood methods
> can offer approximate confidence intervals on the length of a branch.
> If the confidence intervals overlap zero, we know that we are not
> even confident that the branch exists at all.  This is also implemented
> and discussed in PHYLIP and PAUP*.
> 
> >   Also- how does one interpret the vertical and horizontal distances
> >in rooted dendograms as, for example, output from Treeview?
> 
> The distance along a branch from root to tip is often drawn
> proportional to some measure of (possibly corrected) evolutionary
> distance.  Sometimes trees are simply drawn as topologies with
> arbitrary branch lengths, so watch out.  If the tree is in a published
> paper, they should indicate the scale.
> 
> The distance on the page from one tip to another is almost
> always meaningless.  You can rotate parts of the tree to bring
> tips closer together or further apart without having any effect
> on the tree at all--it's just a presentational issue.  (The less
> scrupulous among us may prefer to order the tips in such a way
> as to give more visual support to their preferred groupings!)
> 
> Mary Kuhner mkkuhner at genetics.washington.edu
> 
> ---
The link given above doesn't work, but this one does:
http://courses.mbl.edu/Courses/MOLE.html (maybe because it's case
sensitive). However all of the links provided on this page were down
when I tried it a few minutes ago.....:-(

Hans