February 03, 2012, at 10:08 AM
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----
Other lists
# http://molbiol-tools.ca/molecular_biology_freeware.htm
February 01, 2012, at 04:00 PM
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# Prichard lab
# Stephen lab
# Donelly lab
February 01, 2012, at 12:16 PM
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# http://przeworski.uchicago.edu/software.html
#
February 01, 2012, at 12:11 PM
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----
Population genetics
# http://www.sendou.soken.ac.jp/esb/innan/InnanLab/software.html
October 17, 2011, at 03:41 PM
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----
!!Simulation tools for teaching evolution
* [[http://boxcar2d.com/derpBikeDesigner.html | boxcar2d ]]
* [[http://www.cambrianexplosion.com | simulate species evolution]]
* Avida-ED
evolution games
----
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March 30, 2011, at 11:04 AM
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!! Standalone tools for teaching and research
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# [[ http://www.cytoscape.org/ | Cytoscape]] for networks
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# [[ http://www.cytoscape.org/ | Cytoscape]] for networks
March 30, 2011, at 11:03 AM
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# [[http://www.genome.duke.edu/labs/YouLab/software/dynetica/index.php | Dynetica network simulation Java]]
January 11, 2011, at 09:51 PM
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# http://www.is.titech.ac.jp/~shimo/prog/consel/index.html CONSEL, tree selection
to:
# [[http://www.is.titech.ac.jp/~shimo/prog/consel/index.html | CONSEL, tree selection]]
January 11, 2011, at 09:51 PM
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----
!! Phylogeny
# http://www.is.titech.ac.jp/~shimo/prog/consel/index.html CONSEL, tree selection
January 11, 2011, at 09:09 PM
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# [[http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php | List by Paul Lewis]]
January 11, 2011, at 08:32 PM
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!! Standalone tools for teaching
to:
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!! Other popular educational tools
to:
!! Other popular computing software
# [[http://www.molecularevolution.org/software | Software, molecularevolution.org ]]
April 23, 2010, at 10:47 AM
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# [[http://www.dnai.org/geneboy/ | Gene Boy ]]
November 10, 2009, at 09:34 AM
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# [[http://www.sabiosciences.com/genenetwork/genenetworkcentral.php | Gene network central ]]
May 19, 2009, at 01:28 AM
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# [[http://www.sci.utah.edu/ | SCIRun ]]
to:
# [[http://www.sci.utah.edu/ | SCIRun ]] for modeling and visualization.
May 19, 2009, at 01:20 AM
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# [[http://www.sci.utah.edu/ | SCIRun ]]
May 13, 2009, at 03:07 PM
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# [[ http://www.sagemath.org| SAGE ]] an open-source math tool (equivalent to Maple)
# [[ http://www.scilab.org | scilab]]
to:
# [[ http://www.sagemath.org| SAGE ]] an open-source equivalent of Maple
# [[ http://www.scilab.org | scilab]] an open-source equivalent of matlab
May 13, 2009, at 03:06 PM
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# [[ http://www.scilab.org | scilab]]
May 13, 2009, at 10:54 AM
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!! Other popular educational tools, but I (HQ) am not familiar with.
to:
!! Other popular educational tools
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# [[ http://www.sagemath.org| SAGE ]] an open-source math tool
to:
# [[ http://www.sagemath.org| SAGE ]] an open-source math tool (equivalent to Maple)
May 13, 2009, at 10:53 AM
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# [[ http://www.sagemath.org| SAGE ]] an open-source math tool
May 12, 2009, at 05:00 PM
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# [[http://molvis.sdsc.edu/fgij/index.htm | FirstGlance for protein structure]]
May 10, 2009, at 03:12 PM
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May 10, 2009, at 03:11 PM
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# [[ http://workbench.sdsc.edu/ | Online biology workbench]]
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# [[http://www.neuron.yale.edu/neuron/ | NEURON ]] for empirically-based simulations of neurons and networks of neurons
to:
# [[http://www.neuron.yale.edu/neuron/ | NEURON ]] for empirically-based simulations of neurons and networks of neurons
May 10, 2009, at 03:05 PM
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May 10, 2009, at 03:05 PM
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# [[http://www.neuron.yale.edu/neuron/ | NEURON ]] for empirically-based simulations of neurons and networks of neurons
May 06, 2009, at 10:05 PM
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# [[ http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml | CN3D ]] for protein structure.
May 06, 2009, at 09:54 PM
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!! Other popular educational tools (but HQ is not familiar with)
to:
!! Other popular educational tools, but I (HQ) am not familiar with.
May 06, 2009, at 09:53 PM
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!! Other popular educational tools (but I am not familiar with)
to:
!! Other popular educational tools (but HQ is not familiar with)
May 06, 2009, at 09:43 PM
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!! Other popular educational tools (but I am not familiar with)
# [[ http://caseit.uwrf.edu/caseit.html | CaseIT]] a computer simulation tool that performs common laboratory procedures on any DNA or protein sequence.
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# [[ | Cytoscape]] for networks
!! Other popular educational tools (but I am not familiar with)
# [[ http://caseit.uwrf.edu/caseit.html | CaseIT]] a computer simulation tool that performs common laboratory procedures on any DNA or protein sequence.
# [[http://www.cs.waikato.ac.nz/ml/weka/ | WEKA ]], machine learning and data mining.
to:
# [[ http://www.cytoscape.org/ | Cytoscape]] for networks
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# [[http://www.cs.waikato.ac.nz/ml/weka/ | WEKA ]], machine learning and data mining.
May 06, 2009, at 09:42 PM
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!! Other popular tools (but I am not familiar with)
# [[http://www.cs.waikato.ac.nz/ml/weka/ | WEKA ]], machine learning and data mining
# [[http://www.ks.uiuc.edu/Research/vmd/ | VMD ]] for protein structure
# [[http://utopia.cs.manchester.ac.uk/about-0 | Utopia ]] visualization
# [[http://david.abcc.ncifcrf.gov/ | DAVID Bioinformatics Resources]] at National Institute of Allergy and Infectious Diseases (NIAID), NIH
to:
!! Other popular educational tools (but I am not familiar with)
# [[ http://caseit.uwrf.edu/caseit.html | CaseIT]] a computer simulation tool that performs common laboratory procedures on any DNA or protein sequence.
# [[http://www.cs.waikato.ac.nz/ml/weka/ | WEKA ]], machine learning and data mining.
# [[http://www.ks.uiuc.edu/Research/vmd/ | VMD ]] for protein structure.
# [[http://www.cgl.ucsf.edu/chimera/ | CHIMERA ]] for protein structure.
# [[http://utopia.cs.manchester.ac.uk/about-0 | Utopia ]] visualization.
# [[http://david.abcc.ncifcrf.gov/ | DAVID Bioinformatics Resources]] at National Institute of Allergy and Infectious Diseases (NIAID), NIH.
May 06, 2009, at 09:38 PM
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# [[http://utopia.cs.manchester.ac.uk/about-0 | Utopia ]]
to:
# [[http://www.cs.waikato.ac.nz/ml/weka/ | WEKA ]], machine learning and data mining
# [[http://www.ks.uiuc.edu/Research/vmd/ | VMD ]] for protein structure
# [[http://utopia.cs.manchester.ac.uk/about-0 | Utopia ]] visualization
May 06, 2009, at 09:34 PM
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# [[http://david.abcc.ncifcrf.gov/ | DAVID Bioinformatics Resources]] at
National Institute of Allergy and Infectious Diseases (NIAID), NIH
to:
# [[http://david.abcc.ncifcrf.gov/ | DAVID Bioinformatics Resources]] at National Institute of Allergy and Infectious Diseases (NIAID), NIH
May 06, 2009, at 09:34 PM
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!! Tools that I am not familiar with, but seem to be the choice of others
to:
!! Other popular tools (but I am not familiar with)
May 06, 2009, at 09:33 PM
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# [[ | Cytoscape]] for networks
!! Tools that I am not familiar with, but seem to be the choice of others
# [[http://utopia.cs.manchester.ac.uk/about-0 | Utopia ]]
# [[http://david.abcc.ncifcrf.gov/ | DAVID Bioinformatics Resources]] at
National Institute of Allergy and Infectious Diseases (NIAID), NIH
May 06, 2009, at 09:25 PM
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# [[ http://www.megasoftware.net/ | MEGA4 ]] for phylygeny
to:
# [[ http://www.megasoftware.net/ | MEGA4 ]] for phylogeny
May 06, 2009, at 09:24 PM
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!! Web-based tools for teaching
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!! Standalone tools
# [[ http://www.megasoftware.net/ | MEGA4 ]]
# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]]
to:
!! Standalone tools for teaching
# [[ http://www.megasoftware.net/ | MEGA4 ]] for phylygeny
# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]] for protein structure
May 06, 2009, at 09:23 PM
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# [[http://www.r-project.org/ | R ]]
to:
# [[http://www.r-project.org/ | R statistical programming and environment]]
# [[http://www.ggobi.org/ | GGobi data visualization ]]
May 06, 2009, at 09:21 PM
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# [[http://www.r-project.org/ | R ]]
May 06, 2009, at 09:18 PM
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May 06, 2009, at 09:18 PM
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Web-based tools
# [[http://www.ncbi.nlm.nih.gov/ | NCBI ]]
# [[http://blast.ncbi.nlm.nih.gov/Blast.cgi | NCBI BLAST ]]
# [[http://www.ebi.ac.uk/Tools/emboss/align/index.html | EBI Pairwise seq alignment ]]
# [[http://www.itu.dk/people/sestoft/bsa/graphalign.html | Graphic pairwise seq alignment by dynamic programming]]
# [[http://zucker.limbio-paris13.org/COURS/M1S1-SMBH/Cours2baba.html | Pairwise alignment applet]]
# [[ http://www.ebi.ac.uk/Tools/clustalw/ | EBI ClustalW]]
# [[http://www.cs.umb.edu/~srevilak/viterbi/ | Viterbi Applet, UMB]]
# [[http://weblogo.berkeley.edu/ | WebLogo ]]
# [[http://www.phylogeny.fr/ | Online Phylogeny Construction, Marseille, France ]]
Standalone tools
# [[ http://www.megasoftware.net/ | MEGA4 ]]
# [[http://spdbv.vital-it.ch/| SWISS PDB Viewer ]]
# [[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html | Dendroscope for tree presentation ]]