Karoly Lab Web Resources

"Which DNA Marker
for Which Purpose?"		 Final Compendium of the Research Project "Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees" in the European Union DGXII Biotechnology FW IV Research Programme "Molecular Tools for Biodiversity", E.M. Gillet (ed.), 1999. Includes information about software analysis programs
The Complete Tobacco
cpDNA genome		 This links directly to the GenBank accession for the complete Tobacco cpDNA sequence (from Shinozaki, et al., 1986, The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J. 5: 2043-2049). The uninterupted text of the sequence is availablehere.
NCBI
Home Page		 Access to GenBank and the various approaches for searching the sequence database. Another useful site is the European Bioinformatics Institute.

Software Download		 This link will take you to a BioRad web site which provides the software necessary to read the Quantity One files created by the Fluor-S BioRad scanner in B218. You will need to create an acccount at BioRad and log in to be able to download the software, which can then be used in "Basic" mode without a license..
PCR Primer
Design		 The Primer3 web site at MIT can help you design primers for any known DNA sequence
PCR Primer
Tm calculator		 Integrated DNA Technologies has a primer analysis site that provides Tm and analyses such as self-dimer and heterodimer formation.
PCR Trouble
Shooting		 This site has a flowchart for dealing with problems encountered during PCR.

Restriction
Endonucleases

New England Biolabs' online catalog has information about commonly used restriction enzymes.
ISSR Resource
Web site		 This site is maintained by Dr. Andrea Wolfe at Ohio State Univ. and provides information about the technique as well as methods for data analysis.
Comon Errors
in English		 Just what the well-versed thesis student needs - a site to assist you in avoiding common errors in your writing. check it out.
Modest Advice to Grad Students Dr. Steve Stearns (once a faculty at Reed) wrote these comments back in 1976 for a graduate course at Berkeley. In Feb. 2000, he wrote to the evol.dir list-serv "I would not change a word."
Reed Library
DataBases
  • Web of Science (includ. Science Citation Index)
  • E-journals
    • Data Analysis
    Web Sites
  • Genetic Studio population genetic analyses, including a data editor, results display, and a series of analysis plugins (including standard pop gen summary stats, AMOVA, etc.) .
  • GeoDis v 2.0 Phylogeographic analysis which implements Templeton et al.'s (1995) statistical method for determining the relative contributions to population genetic structure from common ancestry and from current genetic exchange.
  • Arlequin Excoffier's software package for intra- and inter-population genetic data analysis.
  • AMOVA phylogenetic analysis of comparative data (runs in Windows platform). also check the AMOVA-Prep program.
  • TFPGA Tools For Population Genetic Analysis (Windows95).
  • Goodnight Software population genetic software for relatedness and kinship analyses.
  • DAMBE Data Analysis in Molecular Biology and Evolution.
  • CLUSTALW Web-based sequence alignment program from EBI.
  • Genamics SoftwareSeek Repository for tools for use in molecualr biology and biochemistry (including DNA analysis tools)
  • JustBio Repository for tools for use in molecualr biology and biochemistry (including DNA analysis tools)
  • EditView Free software package from Perkin Elmer that lets you view ABI chromatograms (traces) for your sequences.
  • Sequencher Demo Version Software package that can be used for sequence alignment and analysis
  • MEGA Molecular Evolutionary Genetics Analysis: provides statistical and computational methods that parallel those presented in the book Molecular Evolution and Phylogenetics (Nei and Kumar, Oxford University Press, 2000). This book explains various statistical methods for analyzing molecular data and shows how to interpret the results obtained by various computer programs.
    • Northwest Botany
    Web Sites
  • Native Plant Society of Oregon
  • Washington Native Plant Society
  • Oregon State University HerbariumIncludes on-line access to databases for both plants and fungi as well as a link to information on the current Oregon Flora Project
  • Flora NorthwestThis site contains descriptions and pictures of flowering plants in Oregon and Washington and includes a regularly updated list of what can be found in bloom (broken down by region).
  • USDA ForestService Region 6USFS web site for the Pacific Northwest Region
  • H.J. Andrews Experimental ForestThe Andrews Experimental Forest is located in the Oregon Cascades an hour's drive east of Eugene, and is managed cooperatively by OSU and the USFS as an LTER site.
  • Wind River Canopy Crane Research FacilityThe canopy crane facility is located in a Research Natural Area on the Washington side of the Columbia River Gorge.
  • Pacific Northwest Ecosystem Research ConsortiumThis site focuses on providing tools and data that can assist in management decisions regarding ecosystems in the pacific northwest. Included among their datasets is a map of the Willamette Valley's vegetation during the 1850's

    • ACME Mapper This site has all of the USGS topographic maps of the U.S. in a searchable, seamless format.
    Color Landform Atlas
    of the U.S.     		This site from the John Hopkins Univ. Applied Physics Lab has nice topographic state maps.