available tools for alignment and phylogeny

Nicolas Nicolas
Thu May 2 04:30:03 EST 1996

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

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

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