Phylo_win

Brian Foley btf at t10.lanl.gov
Mon Mar 17 16:37:43 EST 1997


Brian Godwin wrote:
> 
> Does anyone know where to get the program Phylo_win for Unix? 


Version 1.2 of phylo_win is available from anonymous ftp at

biom3.univ-lyon1.fr (pub/mol_phylogeny/phylo_win).



The main new features are :

  - trees within PHYLIP files are allowed 

  - tree editor : fonts can be changed, the header can be removed,
    a minimal threshold for displayed bootstrap values can be set.

  - a new distance is available for aminoacid sequences : the PAM
distance
    (from program PROTDIST of the PHYLIP package, use of C code granted
by 
    Joe Felsenstein). Distances are computed assuming that transition
    probabilities between pairs of aminoacids are those of Dayhoff's PAM 
    matrix. 

  - a few bug were fixed.


Comments and/or suggestions about this new version are welcome. Please
note that phylo_win is now available for Linux-PC and VMS systems,
thanks
to Thomas E. Sicheritz Ponten and David Mathog.


Nicolas Galtier
Laboratoire de Biometrie, Genetique et Biologie des Populations
Universite C. Bernard
Lyon
France
galtier at biomserv.univ-lyon1.fr (Nicolas Galtier)

> How about
> Seaview?


SEAVIEW and PHYLO_WIN, two graphic tools dedicated to sequence
alignment and molecular phylogenetics are available by anonymous
ftp to : biom3.univ-lyon1.fr (pub/mol_phylogeny).


SEAVIEW (Manolo Gouy) is an efficient multiple alignment editor. It
allows easy gap insertions/deletions into/from selectable groups
of sequences. Alignment program clustalw (Des Higgins) can be called 
on-line, so that (parts of) the sequences may be automatically aligned.
A dot-plot routine allows an easy matching of similar regions.

PHYLO_WIN (Nicolas Galtier) is a graphic interface for molecular
phylogenetic inference. It performs neighbor-joining, parsimony and
maximum likelihood methods and bootstrap with any of them. Many
distances
can be used including Jukes & Cantor, Kimura, Tajima & Nei, Galtier &
Gouy
(1995), LogDet for nucleotidic sequences, Poisson correction for proteic
sequences, Ka and Ks for codon sequences. Species and sites to include
in the
analysis are selected by mouse. Reconstructed trees can be drawn,
edited,
printed, stored, evaluated according to numerous criteria.

Taxonomic species groups and sets of conserved regions can be defined by 
mouse in both tools and stored into sequence files, thus avoiding
multiple
data files.

Both are entirely mouse-driven. On-line help makes them easy to use.
Most usual sequence file formats are read : CLUSTAL, FASTA, PHYLIP,
MASE.

They run on many Unix WorkStations including Sun (SunOS and Solaris),
Silicon Graphics, IBM, DEC alpha, HP.


For any comment, question, help needed to install, etc... please contact
N. Galtier (galtier at biomserv.univ-lyon1.fr).


Manolo GOUY and Nicolas GALTIER

C.N.R.S. UMR 5558
Universite C.Bernard Lyon 1
Laboratoire de Biometrie, Genetique et Biologie des Populations
43, Bd du 11 novembre 1918
69622 VILLEURBANNE cedex
FRANCE

galtier at biomserv.univ-lyon1.fr   
mgouy at biomserv.univ-lyon1.fr


> Thank you in advance
> Brian Godwin
> 
> P.S. Can you email me your resonse

-- 
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|Brian T. Foley               btf at t10.lanl.gov                       |
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