IUBio

MULTIPLE ALIGNMENTS/TREES SOFTWARE

Nicolas Nicolas
Thu May 16 04:47:02 EST 1996


In article pnf at nntp.Stanford.EDU, Ignacio Marin <marin at cmgm.stanford.edu> writes:
> I am looking for programs to perform multiple alignments of protein 
> sequences plus build phylogenetic trees from these alignments in the 
> net.
>
> Thanks
> 
> Ignacio
 

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.

For any comment, question, help needed to install, etc... please contact

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   








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