Computational Molecular Evolution

This web site was generated for a graduate course entitled Computational Molecular Evolution taught in the Departments of Genetics and Statistics at North Carolina State University (GN756/ST756). The course is taught by William R. Atchley and Jeffrey Thorne. The instructors would appreciate knowing of additional relevant sites or corrections to this page. (Last revision: 8/8/2005). Please report broken links to bill at atchleylab dot org.

Some General References in Computational Molecular Evolution

Course Syllabus
Course Requirements

The following links provide important information for molecular evolution analyses

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

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

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

Bibliographic databases

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

Molecular Modeling

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)

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 for the Study of Evolution
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

Our non-spam e-mail addresses:
bill at atchleylab dot org
thorne at statgen dot ncsu dotedu