Wagner trees

"Daniel Sch?tz" <[email hidden]> wrote in message

Quoted message said:

caused by a project of "Jugend forscht" I want to know how I can reconstruct Wagner trees. Can
someone tell me how to do? Or can > me

someone recommend a computer program that creates such

Quoted message said:

trees?

Here's a link

faculty.virginia.eduwagner trees.htmlOpen ↗

since I'm a computer programmer implementing this looks mainly like donkey work. Since you don't
give your level of experience it is difficult to tell you how to set about it.

The idea of Wagner tree is that we have a list of characters for each organism (tail length, no
toes, skin colour etc), each coded by a small number of integer states. The states are arranged so
that numbers ajacent are most similar to each other - for number of toes the coding is obvious, for
tail length it could be length in inches, for skin colour you would have to assign arbitrary numbers
to grey, brown, and black.

We then calculate a hypothetical ancestor using the most primitive state of all the traits.

To write a computer program you need to decide what sort of interface you will have. The simplest
thing to get the program up and running is to define a text file format, where the user enters the
character matrix and the ancestor. However for a user-friendly program you would need to provide a
graphical interface.

You need to load your matrix. In C it will look like this

struct matrix { int N; /* number of organisms */ int n; /* number of traits */ int **traits; /* 2d
allocated trait matrix */ int *ancestor; /* the ancestor */ };

The next thing you do is find the organism that is most similar to the ancestor. This is
pretty simple.

We then calculate the interval (difference) between the ancestor and the nearest. This is the first
interval on the tree.

Now we need to find the nearest to the interval. If ANC is the ancestor and A is the nearest, the
distance for B =

interval(ANC-B) + interval(A-B) - interval(ANC-A)

Once we have found the best match, we construct the common ancestor of A and B (assume B is the best
match). If ANC A and B have the same state then obviously the hypothetical ancestor (HTU) has that
state. If any two of ANC A and B are the same then HTU takes that state. If ANC A and B are all
different then HTU is the average.

This should be quite easy to code.

Sometimes HTU ends up equal to A, which means that B is derived from A. Otherwise, HTU is placed on
the tree between ANC, A and B.

So we need some sort of structure to represent these intervals. Only binary nodes are allowed.

typedef struct node { node *ancestor; node *child1; node *child2; int *characters; } NODE;

Keep a pointer to the root ancestor, and walk the tree recursively.

Now we have three intervals. We simply repeat the process until we have added all organisms.

"Daniel Sch?tz" <[email hidden]> wrote in message
"]news:[email hidden]...
: Dear NG,
:
: caused by a project of "Jugend forscht" I want to know how I can reconstruct Wagner trees. Can
: someone tell me how to do? Or can me someone recommend a computer program that creates such trees?
:
: If you can help me please answer.
:
: PS: Sorry for my bad English
:
: Ciao
:
: Daniel

Try:

faculty.virginia.eduwagner trees.htmlOpen ↗

Jois

Yes. The program PARS available free at
evolution.gs.washington.eduphylip.htmlOpen ↗ as part of
Felsenstein's PHYLIP software package. It implements the Wagner
parsimony method with multiple states.
For details on how the Wagner parsimony method works see:
Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates, MA.
and the original works on the subject are:
Eck, R.V. and M.O Dayhoff. 1966. Atlas of Protein Sequence and
Structure 1966. National Biomedical Research Foundation, Silver
Spring, Maryland.
(which is probably not widely available)
Kluge, A.G. and J.S. Farris. 1969. Quantitative phyletics and the
evolution of anurans. Systematic Zoology 18: 1-32.

[email hidden] (Daniel Sch?tz) wrote in message
news:<[email hidden]>...

Quoted message said:

Dear NG,

caused by a project of "Jugend forscht" I want to know how I can reconstruct Wagner trees. Can
someone tell me how to do? Or can me someone recommend a computer program that creates such trees?

If you can help me please answer.

PS: Sorry for my bad English

Ciao

Daniel