[Bio-software] Re: Phylip - WinXP

glykokalyx At hotmail.com via bio-soft%40net.bio.net (by glykokalyx At hotmail.com)
Fri Dec 1 11:13:50 EST 2006


Dear Joe Felsenstein,

thank you very much for your reply! And the helpfull advice how to run
it with just 3 sequences.

Regards,
Janosch

> This is a "feature" of Fitch.  You get no result if you have only
> three sequences.  You need at least 4.  My apologies for this
> poor behavior.  However with three sequenceds there is only one
> possible tree topology (a single interior node connected to all
> three).  You can draw the tree by hand.  It is:
>
> (putida:x,LB400:y,HD100:z);
>
> putida      0.000000  0.713185  3.438244
> >LB400       0.713185  0.000000  3.052331
> >HD100       3.438244  3.052331  0.000000
>
> >
> where the three numbers x, y, and z are given by
>
> x = (1/2)(0.713185+3.438244-3.052331) = 0.549549
>
> y = (1/2)(0.713185+3.052331-3.438244) = 0.163636
>
> z = (1/2)(3.438244+3.052331-0.713185) = 2.888695
>
> If you run Neighbor you will get this tree, as Neighbor allows trees as
> small as three species.  The fit is perfect in either case (as there are
> three branch lengths being used to explain three distances.



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