Computational Molecular Evolution

From：www.mdbbs.org

Molecular Biology Databases

• NCBI GenBank
• EMBL
• EMBL - InterPro - Database of protein families, domains and functional sites
• Swiss-Prot and TrEMBL
• Protein Data Bank (PDB)
• UniProt Universal Protein Resource
• OWL Composite Protein Sequence Database
• dbEST cDNA Fragments
• PIR Protein Sequence Database
• TRANSFAC - Gene regulation database
• TIGRFAMs - TIGR protein families db
• Nucleic Acids Research Molecular Biology Database Collection

Some Organismal Data Bases

• Nucleic Acids Research 2005 Organismal Database Issue
• ExPASy's Species Specific Databases
• DBCAT - Public Catalog of Databases
• OMIA - Online Mendelian Inheritance in Aminals
• OMIM - Online Mendelian Inheritance in Man
• MGI - Mouse Genome Informatics
• Yeast Genome Page
• FlyBase - Database of the Drosophila Genome
• The Interactive Fly
• Wormbase - C. elegans Data Base
• tair - Arabidopsis Information Resource
• MIPS - Arabidopsis Data Base
• GeneCards

Protein Interaction Databases

• GenomeWeb - Protein interaction databases
• BIND - Biomolecular Interaction Network Database
• DIP - Database of Interacting Proteins
• MINT - Molecular INTeraction database
• MIPS - Mammalian protein-protein interaction database

Sequence Similarity Database Searching

• Blast Server
• NCBI Blast tutorial
  NCBI Psi-Blast tutorial
• Geospiza Blast tutorial for beginners
• Fasta Server

Protein Motif and Domain Searching

• Motif Search - Kyoto University Bioinformatics Center
• ScanProsite
• InterProScan
• BLOCKS
• PRINTS
• ProDom
• Pfam
• SMART - Simple Modular Architecture Research Tool
• Panther - Protein analysis through evolutionary relationships
• MEME - Motif building
• MAST - MEME motif matching within a protein database
• PROSITE - Build a motif and search
• PROSITE - Generate a prosite or HMMer profile from a multiple sequence alignment
• PROSITE - E nter a sequence and search for prosite, blocks, prodom, prints and pfam motifs
• DomainFinder

Sequence Alignment Tools

• Dialign T
• Chaos-Dialign
• Anchored Dialign
• ClustalW - Software Source
• ClustalW - Alignment submission form
• T-Coffee - Multiple sequence alignment
• Divide and Conquer Multiple Sequence Alignment
• Muscle - Multiple protein sequence alignment at Berkeley
• Squint - Multiple sequence alignment editor
• GeneDoc - Sequence alignment editing software
• Decrease redundancy - Reduces a set of sequences to a non-redundant set
• Cinema - Color INteraction Editor for Multiple Alignments
• AltAVisT - Alternative alignment visualization tool
• Balibase - reference sequence database for studying alignments

Sequence Analysis Tools

• ExPASy Proteomics tools
• EMBL Database searching, browsing and analysis tools
• ProteinPredict Server
• NCBI Molecular Tools
• EBI Tool Box
• Molecular Toolkit
• Mathworks Sequence Analysis Tools
• CMS Molecular Biology Resource
• SAPS - Statistical Analysis of Protein Sequences
• ProtParam
• ProtScale
• PatScan Pattern Scanning
• VAST - Search for a protein's structural neighbors
• Biology WorkBench
• Swiss-Shop - automatically obtain by e-mail new sequences of interest
• RandSeq - Random protein sequence generator
• HMMER - Hidden Markov Modeling; HMMER Documentation

Molecular Visualization

• Molvis
• RasMol
• Protein Explorer
• VMD - NIH Visual molecular dynamics
• MolSoft
• Chime
• PyMOL

Amino Acid Attributes

• AAIndex - Amino acid index database
• Multivariate analysis of amino acid attributes

Bibliographic databases

• PubMed - Entrez
• Pedro's Biomolecular Research Tools
• SeqAnalRef
• Agricola
• iHOP - Links to literature on individual proteins
• Biological Journals and Abbreviations

Some Bioinformatics Sites

• Computational Molecular Biology at NIH
• Bioinformatics Servers
• Computational Biology at Argonne National Laboratory
• Baylor University College of Medicine HGSC
• Bielefeld Bioinformatics Server
• MIPS - Munich Information Center for Protein Sequences
• GOBICS - University of Goettingen Bioinformatics Server
• PhyCom - A Phylogenetic Community
• Rod Page's Server at Glasgow
• University of Oxford evolutionary biology group
• Allan Wilson Center - New Zealand

Molecular Modeling

• Molecular Dynamics Simulations -- Tutorial
• [url=http://bmerc-www.bu.edu/]Boston University (BMERC) Protein Sequence Analysis (PSA)[/url]
• UC Santa Cruz sequence alignment and modeling system (SAM)
• NIH Molecular Modeling Home Page
• Molecular modeling toolkit
• Molecular modeling of proteins
• nMOLDYN

Phylogeny

• MEGA3
• MrBayes
• Beast
• PAML
• PAUP - home page; Quick Start Tutorial
• Brian O'Meara Paup tutorial
• Weighbor - Weighted neighbor-joining
• PHYLIP
• Spectronet - visualization of non-bifurcating tree like complex evolutionary data
• Mesquite - Modular system for evolutionary analyses
• Tree-Puzzle - maximum likelihood analysis of sequence data
• SplitsTree4
• McClade
• Clann - Constructing supertrees
• DAMBE
• HYPHY - maximum likelihood analyses of genetic sequence data
• PHYML - fast algorithm for phylogeny estimation using maximum likelihood
• ModelGenerator - amino acid and nucleotide substitution model selection
• FitModeL - fits substitution models to sequence data using maximum likelihood
• PROTTEST - selection of best-fit models of protein evolution
• Rose - Random model of sequence evolution
• Phyl-o-Gen - Phylogenetic simulation package
• Seq-Gen - Monte Carlo simulation of sequence data along phylogenetic trees
• Rhino - Phylogenetic models for estimating rates and dates
• Pebble
• The Tree of Life
• Treeview
• Time Tree of Life
• Glossary of terms used in phylogenetic reconstruction

Multivariate Statistics Tutorials (from Dr. David Garson's NCSU website)

• Multiple regression
• Factor analysis including principal components analysis
• Structural equataion modeling
• Discriminant analysis

Guides, Tutorials, Courses, Dictionaries and other Resources

• Molecular Biologists Desk Reference
• Codon Usage Tables
• ExPASy BioHunt Search
• Google
• Tree Thinking Group - Phylogenetic analysis in education

Journals and on-line publications in Computational Biology

• Molecular Biology and Evolution
• Journal of Molecular Evolution
• Evolutionary Bioinformatics Online
• PLOS Computational Biology
• Computational Biology and Chemistry
• Bioinformatics
• Nucleic Acids Research
• BMC Bioinformatics
• Journal of Bioinformatics and Computational Biology
• Journal of Molecular Modeling
• Journal of Computational Biology
• BMC Evolutionary Biology
• Journal of Negative Results -- In case your experiment doesn't work out like you had hoped

Other Relevant Sites

• YouSendit - Very useful server for e-mailing very large files
• RefDesk - World's greatest source of facts and links
• ISI Web of Knowledge
• Society for Molecular Biology and Evolution
• International Society for Computational Biology
• Society of Systematic Biologists
• Cosmic Evolution
• Evolution Resources from the National Academies
• BioMed Central
• The Onion
• Trivia - For stuff not covered in our GN/ST 756 course
• SCIgen - Automatic paper generator for those losing out in the publish or perish rat race.
• Bill Atchley's Home Page
• Bill Atchley's Personal Links Page
• Jeff Thorne's Home Page
• Jeff Thorne's Favorite Website
• NCSU Library

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