[rrna][ssu] [lsu]

Visit the Source of This Page's Featured Images at: Comparative RNA Web Site (Left) and Protein Data Bank Web Site (Center and Right)


Molecular Systematics WWW Links
Please note: This page has not been completely updated for some time

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Jump to Links for Molecular Biology Searches, Sequence Alignment, Ribosomal RNA, Protein Structure, Mitochondrial and Chloroplast Genomes, Primer Design, Restriction Enzymes, Transposons, Genomics, Evo-Devo, Phylogenetics, Macintosh Software Archives, Molecular Systematics Journals, Bioinformatics and Biocomputing, Evolutionary Biology Resources, Commercial Biotech Sites

Search WWW

Excite Search
AltaVista Search
Lycos Search
Yahoo - Science:Biology

Molecular Biology Searches

NCBI General GenBank Search
NCBI's Entrez
NCBI Taxonomy Browser
Basic Blast Search
FASTA Programs at Univ. of Virginia
PubMed Search
Entrez PubMed Query
Search and Alignment Tools Tutorial
NCBI GenBank Query Email Documentation
Swiss Protein Site
EMBL Tools
PredictProtein Email Service
Brookaven Protein Data Base
Bioinformatics Databases and Analysis Services
Pedro's BioMolecular Research Tools
Blast Search at Cambridge University
GeneStream Search Site (France)
MBCR Links to Sequence Analysis
Brookhaven National laboratory Biology Page
EBI's Scanps Search Server
SpliceOme Relational Database for Intron-Exon Boundaries
About Inteins

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Sequence Alignment

EBI's ClustalW Alignment Web Server
EBI's ClustalW Online Help with Commonly Used File Formats
VSNS Multiple Alignment Links
BCM Alignment Launcher
HMMER Alignment Software Server
Useful Hyper-Article on HMMER and Multiple Alignment by Sean Eddy
Browse PFAM Alphabetical Collection of Protein Alignments (Constructed with HMMER)
Download 1998 PDF Article on 1313 PFAM Alignments of Proteins
AMAS Server (Multiple Alignment of Protein Sequences)
AllAll: Related peptide sequences
Protein Sequence Alignment -- Prof. Barton at EBI
SAM: Sequence Alignment and Modeling System
Jalview - Java Multiple Alignment Editor for Unix or Windows or View Screenshots
Web Alignment Query (of Two Sequences)
ClustalX Alignment Software FTP Site
DCSE Alignment Software for Unix or DOS
BLOCKS Web Server (Fred Hutchinson Cancer Research Center in Seattle)
CINEMA 2.1 Alignment Software for Unix or DOS
Listing of Protein Alignment Programs
Alignment programs for Sun (Gopher)
Basics of Multiple Alignment (VSNS)
Molecular Biology, Strings, Sequences, Trees, Maps - Lloyd Allison

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Ribosomal RNA

Ribosomal Database Project II
Robin Gutell's RNA Secondary Structure Diagrams
RNA Structure Primer
Yeast tRNA-Phe Structure or Here (Requires Chime Plugin)
The RNA World
RNA Base
Michael Zuker's RNA Website
Zuker's MFold Server
Vienna Web Interface to RNAfold Program
Tinoco Plot Web Interface
Rnadraw RNA Folding Program for Windows
RNA Sequence Editor DCSE Program for Unix or DOS
RnaViz Drawing Program for Linux or Windows (DCSE Format)
Vienna RNA Folding Program for Unix
ESSA RNA Folding Program for Unix
Rod Page's Listing of RNA Folding Programs
DOGMA: Dual Organellar GenoMe Annotator

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Protein Structure

ExPASy Protein Site in Geneva
ExPASy Protein Search
Protein Databank (PDB)
Beginner's Interface to PDB Searching
Protein Structure Course (Password Protected) or 1997, or 1996 Courses Here for Free
The Principles of Protein Structure using the Internet
Protein Crystallography 101
Portions of a Ph.D. Dissertation on Protein Crystallography
The ProDom protein domain database
GDP - Genome Database (Protein Info/Searches)
Interpro Resource for Genomic Proteome Comparisons
Article: Seven Ways of Looking at a Protein
CPE Protein Structure Prediction
The AAA Protein Superfamily Server
Jpred - Consensus Protein Secondary Structure Prediction
Download RasMol and Related Resources
Download MolView Lite for Macintosh
Image Summarizing Protein Synthesis in Eukaryotes

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Mitochondrial Genomes

Mitochondrial Genomics Source Guide
NCBI Organelle Genome Resources
NCBI Metazoan Mitochondrial Genomes as Unranked Classification
NCBI Metazoan Mitochondrial Genetic Codes
OGMP Organellar Genomics
OGMP Listing of Mitochondrial Genomes Sequenced
GOBASE Organelle Genome Database
C. elegans Genome Project Mitochondrial Directory
Origin and Nature of Mitochondria
Software and Publications by Mathieu Blanchette and Colleagues

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Primer Design

PCR Overview
PrimerDesign Documentation
Tm Determination
Whitehead Institute's Primer3 Web Server
CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers (Web-based)
The PCR Primers Database
Long PCR Protocol
Primer/Oligo Design programs for Macintosh
Apple Pi:Primers! Software
Listing of Primer Software
Listing of Mac Primer Software
Invitrogen's Oligo Calculator
Biowire.com's free Jellyfish software (for Windows) Now Includes Oligo Design Options

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Restriction Enzymes

How Restriction Enzymes (RE) were Discovered
Webcutter On-line Tool for Restriction Mapping
RE Overview
Multi-Cut Database of RE Buffers
GCG's Mapsort Utility

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Molecular Mechanisms of Recombination
Transposons: Mobile DNA
Animated Transposition (Requires Plug-in)
Walbot Lab
Mobile Genetic Elements

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Genomes On-Line Database (GOLD)
Genomics at NCBI
Genomics at EBI or FTP Site for Eukaryotes
Genomic Information for Eukaryotic Organisms (euGenes)
A Quick Guide to Sequenced Genomes


The Homeobox Page
Homeotic Genes Explained
Cool Views of Drosophila Homeotic Proteins and Their Expression
Xenopus Molecular Marker Resource
Winged Helix/Forkhead transcription factors
Cnidarian Homeoboxes and the Zootype
Sean Carroll's Lab Page
FlyBase, FlyView, FlyLab, FlyBlast, NCBI's Drosophila Genome Page, FlyGenome, Image Database of Gene Expression Patterns in Fly, FlyChromosomes, FlyBrain, or the Interactive Fly,
Boston Evo-Devo Resources
Evo-Devo Articles by Taxon or Concept
Evo-Devo Learns a Larval Lesson
Developmental Mechanisms Problem Set
HOX-Pro Homeobox Genes Database
Berkeley's New Evo-Devo Center
How Limbs Evolved From Fins
How Insects Lost their Legs
Scott Gilbert's Evo-Devo Course
Free Downloads of Evo-Devo Articles in PNAS

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Felsenstein's Directory of Phylogeny Programs
Tree of Life List of Phylogeny Programs
PAUP* Website, Quick Start Tutorial V. 1 (.pdf Format), Command Reference Doc V. 2 (.pdf Format)
Tutorials for PAUP*, Clustal X, etc.
Likelihood-Based Tests of Topologies in Phylogenetics
MrBayes (Phylogenetic Analysis Program using Bayesian Inference) - See also: 1 - 2 - 3 4 - 5 - 6 - 7 - 8 - 9 - 10
IUBio Software and Data
IUBIO Molecular Biology Mac Software
Univ. of Glasgow Systematics Software Listing
Download Component 2.0 (Windows) Now Free
Software Listing from Paul Harvey's Group at Oxford
Gogarten and Lewis Course on Computer Methods in Molecular Evolution
Paul Lewis Course on Phylogenetics
Workshop on Molecular Evolution Schedule and Lectures
Likelihood Ratio Test
Natural History Museum's Molecular Systematics and Evolution of Microorganisms
Programs for Phylogenetics and Population Genetics
Sequence Analysis Tutorials
VSNS HyperText Coursebook Chapter on Molecular Phylogenetics
Genetics Computer Group (Wisconsin GCG)
Wisconsin GCG Tutorials
Codon Usage Tabulated from GenBank (CUTG)
AnnHyb Sequence Utility Software for Windows
Ziheng Yang's Program, PAML: Phylogenetic Analysis by Maximum Likelihood
Pittsburgh Supercomputing Center Sequence Analysis Programs Installed
Oxford Molecular Group's (GCG, SeqLab)
Download PC Versions of Phylogenetics Programs, TNT, NONA and WINCLADA
DAMBE Site (for Windows)
Web and Downloadable Versions of LVB: Reconstructing Evolution with Parsimony and Simulated Annealing
Paul Lewis's Software including Population Genetics Package GDA
Paul-Michael Agapow's Software and Scripts
Barry Hall's Phylogenetic Trees Made Easy Site

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Macintosh Software Archives

U of Mich. Gopher to Mac Archive + Mirrors
U Mich Mac Archive Mirror (ftp)
INFO-MAC HyperArchive ROOT
Chemistry software for the Mac

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Selected Molecular Systematics Journals

Molecular Phylogenetics and Evolution (On-campus Browsing)
Molecular Biology and Evolution (Abstracts Only)
Cladistics (On-campus Browsing)
Evolution (Free Temporary Access)
Systematic Biology (1998 to Present) or Here for Some Abstracts and Data Sets 1995-99

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Bioinformatics and Biocomputing

What is Bioinformatics?
Some Basic Molecular Biology
Molbiol.net Molecular Biology Tools
Baylor's Database and Search Tools
San Diego Supercomputer Center (CMS) Molecular Biology Resources
Bioinformatics Resources
Bioplanet Links to Informatics Resources on Web
Internet-based Courses in Bioinformatics
A Practical Guide to Protein Sequence Analysis
VSNS BioComputing Division (On-line Courses and Resources)
Boston University Bioinformatics Program
Computational Genomics Course at Univ. of Virginia
Sequence Analysis and Comparison: A Bibliography (Last Updated Feb., 1995)
Phylogenetic Analysis Computer Programs
Compute pI/Mw
WWW Links Related to Viruses
TIGR Genomic Databases
TIGR's Links to Genomic Centers
Baylor's Human/Mouse/Fly Genomic Databases
Sanger's Links to Genome Centers
Sanger's Links to Model Organisms
Agricultural Genome Information
Access Excellence
SNAP Program for Synon./Nonsynon. Calculations
VESPA Program for Amino Acid Frequency Comparisons
4Peaks Native Mac OS X Freeware Program for Viewing/Editing Sequence Trace Files
Genetic Science Learning Center

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Evolutionary Biology Resources

Prof. Eernisse's Links to History of Life
Prof. Eernisse's Biology 404 Links to Evolutionary Biology
Lots of Links to Evolution-related Sites
Time line of Evolutionists (under construction)
An Introduction to Evolution
Summaries of Evolutionary Biology Topics
Willi Hennig Society Homepage
Galapagos - Charles Darwin Research Station
Talk.origins Archive Home Page

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Commercial Biotech Sites

Commercial Resources
Bio Online: Biotechnology: Companies
On Line Ordering for Biologists/Biochemists
BioSupply Net
Company Locator
Fisher Scientific
Promega Corporation Home Page
New England BioLabs
Qiagen Product Guide
Amersham-Pharmacia Biotech (North America)
Invitrogen's Topo-TA Cloning Kit
Sequencher Software (Gene Codes Corp.)
Pipetter Repair and Calibration (Southern Instrument Maintenance Co., Arizona)
Biowire Product/Service Reviews and Free Software (Free Laser Pointer for Registering)
CSU Northridge DNA Sequencing Facility
Lark Technology Sequencing Services
Color Digital Image 8"x10" Prints for $3
FinchTV 1.2, a free cross platform trace viewer
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Jump Back to Links for Molecular Biology Searches, Sequence Alignment, Ribosomal RNA, Protein Structure, Mitochondrial and Chloroplast Genomes, Primer Design, Restriction Enzymes, Transposons, Genomics, Evo-Devo, Phylogenetics, Macintosh Software Archives, Molecular Systematics Journals, Bioinformatics and Biocomputing, Evolutionary Biology Resources, Commercial Biotech Sites

Back to Bio 402 Home Page

Douglas J. Eernisse deernisse@fullerton.edu

CSU Fullerton, Biological Science Home Page

The links on this page were last checked on 12/21/00 and last updated on 5/7/06.
If you find broken links or if you find additional cool sites that are appropriate,
please send them and the Web address for this page to Prof. Eernisse.