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(last updated 3/02)
Multiple
Alignment Guides and Tutorial
Database Searching
Tools
Multiple
Alignment
Protein
Families/Motifs/Domains
Protein Analysis
Tools
Phylogeny
Guides
and Tutorials to Biocomputing
Algorithms
For Multiple Sequence Alignments
ClustalW:
multiple sequence alignment.
EMBnet
Biocomputing Tutorials
Guide to Sequence Analysis
*Introduction
to making and using protein multiple alignments
Pasteur
Institute: Guides, Tutorials and Documents
Primer on Molecular Genetics
Principles of Protein Structure
Database
Searching Tools
BCM
Search Launcher: General Protein Sequence/Pattern Searches.
Fasta3
Database Searches at the EBI.
MassSearch:
Searching SwissProt or EMBL by protein mass after digestion.
**PROWL
(protein searches) at Rockefeller - sequence and pattern searching
Multiple
Alignment
AMAS:
Analyse Multiply Aligned Sequences.
*BCM
Search Launcher: Multiple Sequence Alignments.
Biology
WorkBench - Alignment tools.
DCA:
Divide-and-Conquer Multiple Sequence Alignment.
FHCRC:
Block vs Block Searcher using LAMA.
FUNDP:
Match-Box server.
**GeneBee:
Multiple Sequence Alignment.
MSA
: Multiple Sequence alignment using MSA version 2.1
*Multalin
: Multiple sequence alignment by Florence Corpet.
*MultAlign:
Multiple Sequence Alignment Tools.
Protein
Families/Motifs/Domains
BLOCKS
(Protein Motifs).
MOTIF:
Searching Protein Sequence Motifs.
Pfam:
Pfam is a high-quality comprehensive collection of protein domain
families.
PRINTS:
Protein Motif Fingerprint Database.
ProDom:
The protein domain database
PROSITE
is a method of determining what is the function of uncharacterized proteins
translated from genomic or cDNA sequences.
Protein Analysis
Tools
ProtParam
tool (physical computation of proteins).
Phylogeny
Phylogenetic
Software
MacClade
: MacClade is a computer program for phylogenetic analysis.
PAML
(Phylogenetic Analysis by Maximum Likelihood).
PHYLIP
: PHYLIP is a free package of programs for inferring phylogenies.
TreeView
: TreeView is a simple program for displaying phylogenies on Apple
Macintosh and Windows PCs. Documentation
for TreeView
Phylogeny
Sites and Databases
Entrez
Taxonomy Browser
Evolution
and Phylogeny Laboratory: This laboratory provides various
software packages for phylogenetic analysis as well as multiple
sequence alignment.
Evolution
Home Page : This is a site for various projects in evolution,
molecular evolution and phylogenetic epidemiology.
IUBIO
archive: This is a user-supported archive for biology software and data.
Phylogenetic
Analysis Computer Programs
Phylogenetic
tree prediction : Putative phylogenetic trees prediction for
sequence multiple alignment by cluster and topological
algorithms.
Phylogeny
Programs
The
Tree of Life : The Tree of Life is a project designed to
contain information about the phylogenetic relationships and
characteristics of organisms, to illustrate the diversity and
unity of living organisms, and to link biological information
available on the Internet in the form of a phylogenetic
navigator.
TreeBASE:
A Database of Phylogenetic Knowledge.
TreeGen
: Tree generation from distance data.