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Please help... got to make a phylogenetic tree (within 2 days), don't know how..

Raf Podowski Raf.Podowski at cgr.ki.se
Mon Jun 5 14:50:39 EST 2000


Have you tried phylo_win?  It's a great program with many options.  It accepts
alignments in clustal, fasta, phylip and mase format and allows you to
bootstrap and jumble as well as select only a set of sequences and regions to
tree.  Neighbor joining and Max. parsomony trees are available.

Here is the web site.  Binaries are available for a number of architectures.

http://pbil.univ-lyon1.fr/software/phylowin.html

If you want to continue with Phylip, documentation is here:

http://evolution.genetics.washington.edu/phylip.html

Good luck,

Raf Podowski
Center for Genomics Research
Bioinformatics Unit
Karolinska Institute
Stockholm, Sweden



Sander Heijs wrote:

> Hi,
>
> I hope somebody can help me with this problem....I've got several sequences
> (DNA, 16 S) of various length in a text file, together with sequences of
> know species (one text file with 60 species, one with 123 species). I've
> made an important presentation in four days in France on which I want to
> show the phylogenetic trees of these sequences. I've tried using programs as
> phylip (but I don't know how it works...and nobody in our department can
> tell me) and treeconw. The seqeunces are alligned with a program called
> clustalX and converted to Phylip format and Treecon format. I really would
> like to know how to use Phylip...(anybody can send me an e-mail of the
> sequence of progs to use for constructing a tree with as starting point an
> interleaved allignment ?). Treeconw seems a nice program, but when
> calculating distances with bootstrap values the program crashes (don't know
> why...tried removing some sequences and then it works ok....but some very
> important (my own) sequences also make the prog. crash...perhaps they are
> too short ??? app. 100 basepairs...whereas others are about 700..).
> If anybody could help I would be very gratefull....so hope to hear
> anything....
>
> With regards,
>
> Sander Heijs
> University of Groningen
>
> Please reply to: s.k.heijs at biol.rug.nl or s_k_heijs at hotmail.com
> ________________________________________________________________________
> Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com
>
> ---







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