mirror of
https://github.com/Ponce/slackbuilds
synced 2024-10-07 11:07:00 +02:00
32 lines
1.3 KiB
Text
32 lines
1.3 KiB
Text
SeaView is a multiplatform, graphical user interface for multiple
|
|
sequence alignment and molecular phylogeny. Important features are:
|
|
|
|
1) SeaView reads and writes various file formats (NEXUS, MSF,
|
|
CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences
|
|
and of phylogenetic trees.
|
|
|
|
2) SeaView drives programs muscle or clustalw for multiple sequence
|
|
alignment, and also allows to use any external alignment algorithm
|
|
able to read and write FASTA-formatted files.
|
|
|
|
3) Seaview drives the Gblocks program to select blocks of
|
|
evolutionarily conserved sites.
|
|
|
|
4) SeaView computes phylogenetic trees by
|
|
a) parsimony, using PHYLIP's dnapars/protpars algorithm,
|
|
b) distance, with NJ or BioNJ algorithms on a variety of
|
|
evolutionary distances,
|
|
c) maximum likelihood, driving program PhyML 3.0.
|
|
|
|
5) SeaView draws phylogenetic trees on screen, PDF or PostScript files
|
|
6) SeaView allows to download sequences from EMBL/GenBank/UniProt
|
|
using the Internet.
|
|
|
|
For details and citation:
|
|
Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a
|
|
multiplatform graphical user interface for sequence alignment and
|
|
phylogenetic tree building. Molecular Biology and Evolution
|
|
27(2):221-224.
|
|
|
|
This requires fltk as a build dependency, but you also need clustalw,
|
|
Gblocks, PhyML, and muscle, all of which SeaView drives.
|