Biology Labs - OnlineLabs.in - Virtual laboratory simulations for science education. Below is a list of freely available online biology lab resources, including microscopy, genetics and life science. General biology and virtual labs The Interactive Library – This EdInformatics.com site is a list of links to interactive biology sites. Some Java applets are standalone and some come with lesson plans and notesJohnson Explorations – Online explorations from The McGraw-Hill Companies. Interactive simulations for high school biology classes. Alternate links: 1, 2TryScience.com – Variety of online experimentsThe Biology Place: Classic Edition – A free website appropriate for regular and advanced biology.
Anatomy, physiology and dissection See the list of Anatomy Labs Microscopy, cells and microbiology Genetics and DNA Health, medical treatment and blood types Interactive Health Tutorials – From U.S. Population biology and dynamics Animal behavior, evolution and life science The following biology laboratory simulations and educational learning exercises are available for a fee. Genetic Simulation Resources - list. Softlinks - Evol.Mol softwares list (Sergios-Orestis Kolokotronis) FELSENSTEIN's Phylogeny and genetics Programs list. Here are 392 phylogeny packages and 54 free web servers, (almost) all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly monthly.
Here is a "waiting list" of new programs waiting to have their full entries constructed. The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses.
If you discover any inaccuracies, or feel that I have left any important programs or facts out, or if links do not work properly, please e-mail me at: (joe (at) gs.washington.edu). ... by methods available ... by computer systems on which they work ... cross-referenced by method and by computer system. Softwares list UWashington. This list is by no means complete or even exhaustive. At the bottom of the page, there are some other lists you may want to consult. New programs appear almost monthly (most published in Molecular Ecology Resources), so stay aware of developments in the field.
With all programs, always read the original paper and the manual before use. General Purpose Programs These programs are a collection of tests and methods commonly used in population genetics Arlequin General purpose package that does almost every analysis in the book, and accepts microsatellite, allozyme, sequence and other data. PowerMarker Potentially powerful program that calculates all sorts of genetic distances and also does a few other things that no other program does. Genetix Powerful analysis package for population genetics, but you have to understand French. Estimation and Test of Population Genetic Parameters Calculates FST, RST and tests the estimates, among other standard population genetics statistics.
ChiFish PowSim Pedant. Softwares list UWashington 2. Popgen and phylogeny softwares list (Aguirre Lab) The following is a list of some of the sites related to DNA applications that I have found useful at one time or another. If you think I am missing a key site(s), please let me know. Enjoy! Primary: The National Center for Biotechnology Information DNA Sequence Alignments: DNA Sequence Editors/Chromatogram-DNA Visualization: BioEdit - Nice program for editing DNA sequences Chromas Lite - Program for editing DNA sequence chromatograms Convert - Program for converting between common data formats Phylotree - Phylogenetic tree of global human mitochondrial DNA variation Primer Design/PCR tips: Restriction Enzymes/Digestion Predictions: Population Genetics/Structure Software: Phylogenetics Software: Haplotype/Network Mapping Software: Network (from Fluxus Engineering) Microsatellite Scoring/Identification Tools: GeneMarkerGeneScanView - Nice little shareware program for scoring micrsatellites MSATCOMMANDER - Software for locating microsatellites from genome data Useful Commercial Sites/Programs:
Population Genomics and Bioinformatics - Population Genetics Visualization Tools. I would like to share a list of tools that visualize population genetics processes. First, let me share an amazing story from John Turner, Emeritus Prof. of Univ. of Leeds about tools that visualize evolution. This story took place in 1968 in University of York: "My compliments on your putting up that compilation on the web. You may be amused to know that I encountered the same problem many years ago, around 1968 in fact, when computers did not produce graphics, and had in fact had only recently started to be built with transistors rather than thermionic valves. I wanted animations of the curve of gene frequency against time etc for natural selection, for teaching.Solution: we made up movable graphs from transparent film, paper, cardboard, etc, and then filmed them with, e.g. a black invisible mask being withdrawn across the graph. Many thanks to the Evoldir members who provided the information: Andres J.
For some tools I post information found in their webpages. University of Bern - Population Genetics softwares. Here you can find the different software produced by people in the lab and by past members: fastsimcoal2: a much faster continuous-time implementation of simcoal2, based on a sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity along large genomic regions under complex evolutionary histories, and this for for both present or ancient samples.
New version (2.0) is available. BayeScan: a software to detect natural selection from population-base genetic data. New version (2.0) is available. Arlequin: an integrated software package for population genetics data analysis. New version (3.5) is available. University of Bern | Institute of Ecology and Evolution | Baltzerstrasse 6 | CH-3012 Bern | Tel +41 31 631 45 11 (Secr) | Fax +41 31 631 48 88. Softlinks - PopGen softwares list (Sergios-Orestis Kolokotronis) Softlinks - Microsat softwares list (Sergios-Orestis Kolokotronis)
Phylogenetics Softwares list (Taxonomy Zoology UK) This is a list of some taxonomic and phylogenetic software, with emphasis on tree building and molecular data. There are also links to other, more extensive collections that may have what you're looking for if you can't find it here. Contents Tree viewing Tree building Tree comparison and interpretation Sequence format converters Sequence alignment, analysis, and searching RNA secondary structure Software archives Tree viewing TreeView View NEXUS and PHYLIP format tree files on Macs (68K and Power Mac) and Windows (16 and 32 bit). TreeExplorer View and manipulate MEGA format trees under Windows. Tree building Collection of APL Functions for Cladistic Analysis, written by Rino Zandee. Standard program for phylogenetic analysis (currently Macintosh only but PAUP* for PowerMac, DOS, and Unix is coming).
The most comphrehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood, and distance methods, plus utility programs. U.K. mirror site for PHYLIP Spectrum TreeMap. Softlinks - Phylogeny softwares list (Sergios-Orestis Kolokotronis) Softlinks - Alignment softwares links (Sergios-Orestis Kolokotronis) Phylogenetic softwares (Berkeley)