SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny

TLDR

SEA VIEW and PHYLO_WIN are graphic tools for X Windows‑Unix computers that facilitate sequence alignment and molecular phylogenetics. SEA VIEW offers a sequence alignment editor with manual or CLUSTALW‑based automatic alignment and a dot‑plot routine for large sequences, while PHYLO_WIN builds phylogenetic trees using neighbor‑joining, maximum parsimony, and maximum likelihood with bootstrap analysis, and provides tree editing, printing, storage, and evaluation—all within a mouse‑driven interface with online help. Both tools are freely available via anonymous FTP or web download, and can also be requested by e‑mail.

Abstract

SEA VIEW and PHYLO_WIN are two graphic tools for X Windows-Unix computers dedicated to sequence alignment and molecular phylogenetics. SEA VIEW is a sequence alignment editor allowing manual or automatic alignment through an interface with CLUSTALW program. Alignment of large sequences with extensive length differences is made easier by a dot-plot-based routine. The PHYLO_WIN program allows phylogenetic tree building according to most usual methods (neighbor joining with numerous distance estimates, maximum parsimony, maximum likelihood), and a bootstrap analysis with any of them. 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 and stored into sequence files, thus avoiding multiple data files. Both tools are entirely mouse driven. On-line help makes them easy to use. They are freely available by anonymous ftp at biom3.univ-lyonl. fr/pub/ mol_phylogeny or http://acnuc.univ-lyonl.fr, or by e-mail to [e-mail].