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Contents


DROSOPHILA
MAJOR DATABASES
GENOMES
SOFTWARE
SEQUENCE SIMILARITY SEARCHES
ALIGNMENT
SELECTED PREDICTION SERVERS
BIBLIOGRAPHY DATABASES
JOURNALS
GENERAL RESOURCES
OTHER LINKS OF INTEREST


DROSOPHILA

FlyBase (Drosophila database) (UK)  (US)  -  (Japan)
Berkeley Drosophila Genome Project Group
Web Directory: Drosophila Virtual Library
Homophila
TIGR Drosophila gene index
Dosage Compensation in Drosophila
Drosophila Aberration
Flyview
Flybrain

Education:

Interactive Fly
BBC NEWS: Fruit Fly gene success
Zoom the Fruit Fly

Books:

Progress and Prospects in Evolutionary Biology: The Drosophila Model Jeffrey R. Powell (Oxford Univ., Sep 1997)
Genetic Variations of Drosophila Melanogaster
L. Lindsley (Carnegie Inst. of Washington, Dec 1968)
Drosophila subobscura: biology, genetics and inversion polymorphism
Costas B. Krimbas (Kovaéc)
Drosophila Inversion Polymorphism
Costas B. Mrimbas, Jeffrey R. Powell (CRC Press, Aug 1992)
Genome of Drosophila Melanogaster
Dan L. Lindsley, Georgianna G. Zimm (Academic Press, Jan 1992)

Articles:

Release 3 of the Drosophila genome

Research Resources for Drosophila: the expanding universe

 

MAJOR DATABASES

  • Major Public Sequence and Protein Databases

 

GENOMES

 

SOFTWARE

  • General resources and Software information
The Software Biocatalog
Biological Software
Molecular Evolution Software (Oxford University)
Phylogenetic Software
  • Research Software

        DnaSP; DNA Sequence Polymorphism
        DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), and Fu and Li (1993) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent.

        Kinship
        A program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population.

        LAMARC - Likelihood Analysis with Metropolis Algorithm using Random Coalescence
        Package of programs for computing likelihoods for samples of data (DNA sequences and electrophoretic polymorphisms) from populations. Programs use coalescence theory, and estimate population parameters like effective population size, growth rate, and migration rate.

        MacClade
        A friendly Macintosh program primarily for analysis of categorical or state characters. Includes spreadsheets and graphical manipulation of trees.

        MEGA

        The Tree of Life (Phylogeny)

        PHYLIP: Phylogeny Inference Package (J. Felsenstein)

        PhylPro
        Phylogenetic Profile methods for detecting genetic recombination.

        POPGENE: Software for Population Genetics Analysis
        Program designed for the analysis of co-dominant and dominant markers using haploid and diploid data. POPGENE computes both comprehensive genetic statistics (e.g., allele frequency, gene diversity, genetic distance, G-statistics, F-statistics) and complex genetic statistics (e.g., gene flow, neutrality tests, linkage disequilibria, multi-locus structure).

        Relatedness
        Calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs. It finds standard errors and confidence intervals for signifiance testing using a jackknife resampling method.

        Goodnigth software: Recopilation of other software for population biology

        RAPDistance  
        (John Armstrong, Adrian Gibbs, Rod Peakall, Georg Weiller)

        SiScan
        "Sister-scanning" to identify recombination in sequence data.

        TFPGA - Tools for Population Genetic Analyses
        Windows program for the analysis of allozyme and molecular population genetic data. This program calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses.

        Spectrum
        A Mac program designed to read in a data file comprising aligned character
        arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform somesimple spectral analysis procedures on that data.

        Structure
        The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs and SNPs.

        TreeMap
        Experimental program for comparing host and parasite phylogenies. Reads PHYLIP and PAUP tree files, and data COMPONENT files. Program comes with example data files and documentation in Postscript. The versions for the Mac and for Windows are essentially identical.

        TreeView
        Tree drawing software

        VOSTORG
        A package of microcomputer programs for sequence analysis and construction of phylogenetic trees.

        WinAMOVA v 1.55
        A graphical Windows 3.x program for the analysis of population genetic structure from molecular or conventional genetic data. This program is also embedded
        into Arlequin.

 

  • Educational Software
"Game Theory"
demonstrates the simple Hawk/Dove/Bourgeois game designed to provide an example of the use of game theory in evolutionary theory.
GENUP
Computer-aided learning for quantitative genetics and its applications to animal breeding
 
GREGOR
Software for genetic simulation

FSim
Tool for learning about the effects of inbreeding. Simulates a population with varying levels of inbreeding.

PopGen: Population Genetic Simulator
Simulates deterministic and stochastic Population Genetics processes in a one locus, two allele system.

Populus: Population Biology Simulator
Includes simulation of Population Genetics processes.

Selection
 A straightforward population-genetic simulation demonstrating the effects of selection, drift, mutation and migration on allele frequencies in a single-locus, two allele system.

Sex Ratios

A simple simulation programming for demonstrating Fisherian selection on the sex ratio. The interface is patterned on that of "Selection"

Simul8 & PopGen; Genetic simulation program

"This is a one-locus, two-allele genetic simulation program for use by students.

ThetaSim

Tool for learning about the effects of genetic drift. "Successive generations of pure random mating are simulated, and the resulting increase in identity by descent of genes within populations is shown graphically.

Biology Educational Software FAQ

Document that reviews educational software and provides information on how to obtain it. Includes links and information of free and commercial software on Ecology, Evolution, Genetics, and other biological areas. By Eli Meir and the Biology Education Software Taskforce of the University of Washington.
 
  • Other Software

 

SEQUENCE SIMILARITY SEARCHES

EBI FASTA (UK)
NCBI BLAST (Basic Local Alignment Search Tool)

 

ALIGNMENT

  • Pairwise Sequence and Structure Alignment

Pairwise protein alignment (SIM)
BCM Search Launcher (pairwise sequence alignment)
DIALIGN (alignment program without explicit gap penalties)

  • Multiple Alignment and Phylogeny
ClustalW (multiple sequence alignment at BCM)
ClustalW (EBI)
MultAlin 

 

SELECTED PREDICTION SERVERS

  • Gene Finding and Intron Splice Site Prediction

BCM Genefinder
NetGene (prediction of intron splice sites in human genes)
GRAIL interface (protein coding regions and functional sites)

Swiss-Model
PredictProtein

 

BIBLIOGRAPHY DATABASES

The Drosophila Virtual library
PubMed

BioMedNet
Elsevier Science
CSHL press
Frontiers in Bioscience
eLibraries
Biological Sciences Library
Human Genome Project journal´s list
The Virtual library: Bio Sciences

 

JOURNALS

Annual Review of Ecology and Systematics
Annual Review of Genetics
BioInformatics
Bioinform Newsletter
Cell
Current Biology
Current Genetics
Current Opinion in Genetics and Development
Cytogenetics and cell genetics
Development Genes and Evolution
Evolution
Gene
Genes and Development
Genetics
Genome Research
Genomics
Journal of Computational Biology
Journal of Classification
Journal of Evolutionary Biology
Journal of Molecular Biology
Journal of Molecular Modelling
Molecular Biology and Evolution
Nature
Nature Genetics
Nucleic Acids Research
Proceedings of the National Academy of Sciences USA
The international society for computational biology
Trends in Ecology and Evolution
Trends in Genetics
Science
Scientific American
Systematic Biology
THE SCIENTIST

 

GENERAL RESOURCES

The Darwin-L Web Server
The origin of species - Charles Darwin
Population Genetics Links
Biopages (Evolutionary Biology Resources)
The selectionist/neutralist controversy
EvolDir
Phylogenetic Resources (UCMP)
Sites of Interest to Botanists, Ecologists, and Evolutionists
The Tree of Life
Web Resources in Molecular Evolution and Systematics
BIOINFORMATICS: General Resources, Articles, Books and Glossaries (ordered by year)

 

OTHER LINKS OF INTEREST

  • Courses and Degree Programs in Bioinformatics/computational biology
Biocomputing course resource list: course syllabi
Algorithms in molecular biology
Curso de Biocomputación - U.A.B
Curso de Bioinformática - e-biointel  
Boston University (Boston, MA) - MS/PhD
George Mason University (Fairfax, VA) - MS/PhD
Georgia Tech (Atlanta, GA) - MS
Iowa State University (Ames, IA) - PhD
Rutgers University (New Brunswick, NJ) - PhD
University of the Sciences in Philadelphia (Philadelphia, PA) - MS
  • Bioinformatics and Computational Books
Artificial Intelligence and Molecular Biology
Bioinformatics; The Machine Learning Approach
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
Computational Methods in Molecular Biology
Introduction to Computational Biology
Developing Bioinformatics Computer Skills
Beginning Perl for Bioinformatics
Mastering Perl for Bioinformatics
Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition (Baxevanis)
Bioinformatics Computing (Bergeron)
A Primer of Genome Science (Gibson & Muse)
 
  • Bioinformatics News and Articles
Lincoln Stein's Keynote: Building a Bioinformatics Nation
Ewan Birney's Keynote: A Case for Open Source Bioinformatics
Beginning Bioinformatics
An Interview with Ewan Birney: Keynote Speaker at O'Reilly's Bioinformatics Technology Conference
An Interview with Lincoln Stein
O'Reilly Network -- Bioinformatics Technology Conference Coverage
  • Bioinformatics Scientific Articles
University bioinformatics programs on the rise (Zauhar)
A permanent education (Gavaghan)
Training in a hybrid discipline (Wickware)
Creating a bioinformatics nation (Stein)
Can we integrate bioinformatics data on the Internet?
Human Genetics on the Web
The Molecular Biology Database Collection: 2005 update (Galperin) ||  Database Listing
The Nucleic Acids Research Web Servers issue: 2004
XML, bioinformatics and data integration (Achard)
A classification of tasks in bioinformatics (Stevens)
Storing biological sequence databases in relational form (Xie)
Nucleotide sequence databases: a gold mine for biologists (Pandey)
Bioinformatics Tools for Whole Genomes (Searls)
  • Video Sessions
NIH VideoCasting
C-SPAN and C-SPAN2
The Library of Congress
Medical Computing Today (MCToday) Online Medical Events
The University of Chicago






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