I have produced several software packages that are distributed for free.

1. MCLEEPS
2. NewHybrids
3. ChromoSeg
4. GFMCMC (library)
5. MDBlocks

 

• MCLEEPS, Monte Carlo Likelihood for Estimation of Effective Population Size. This implements an importance sampling algorithm to estimate a population's genetically effective population size from temporally spaced samples. The algorithm is described in Anderson, E.C., Williamson, E.G. and Thompson, E.A. (2000) Monte Carlo evaluation of the likelihood for N_e from temporally-spaced samples. Genetics 156: 2109-2118. [abstract] [reprint in pdf (316 K)]. Downloads of this program (which was co-authored by me and Ellen Williamson) are available from its download page at the Universtiy of Washington.

   

• NewHybrids. This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories. The method is described in Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217--1229. [abstract] [reprint in pdf (232 K)].
  • A new release is available April 7, 2003. Version 1.1 Beta 3. This has a number of new features including expanded AFLP support, options for specifying species origins of select individuals, facilities for setting allele frequency priors, a non-graphical user interface version, etc. Download the documentation below for more info.
  • This program uses my GFMCMC visualization library. Click on the icon to see a full-size screen shot.

    Program	Platform/Description	Size	Download
    VERSION 1.1 Beta 3	VERSION 1.1 Beta3
    New Hybrids	Macintosh Classic (OS 9)	470 k	NewHybs1_1Beta3.sit (Stuffit archive with everything you need---all the documentation and test data sets.
    New Hybrids	Windows	613 k	NewHybs1_1PC_Beta3.exe (self-extracting archive with everything you need---all the documentation and the test data sets. Note: you will probably need to download glut32.dll from elsewhere on the web to make this run. That is described in the documentation.)
    New Hybrids	Documentation	183 k	new_hybs_doc1_1Beta3.pdf (the user documentation. This is included in the archives above, but you might wish to download it separately.)
    VERSION1.0	VERSION 1.0		VERSION 1.0
    NewHybrids	Macintosh Classic (OS 9)	424 k	NewHybrids_Mac.sit (Stuffit archive with everything you need---all the documentation and the test data sets.)
    NewHybrids	Windows	416 k	NewHybrids_PC.exe (self-extracting archive with everything you need---all the documentation and the test data sets. Note: you will probably need to download glut32.dll from elsewhere on the web to make this run. That is described in the documentation.)
    NewHybrids	Source Code	216 k	Included in the tarball "EricCode.tgz" which also includes the source code for GFMCMC, ChromoSeg, and Pedagog.
    NewHybrids	Documentation	140 k	new_hybs_doc.pdf (the user documentation. This is included in the archives above, but you might wish to download it separately.)

•  ChromoSeg. A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. There is no user documentation as of yet.
  • This program also uses the GFMCMC library. Click on the icon to see a full-size screen shot.

    Program	Platform/Description	Size	Download
    VERSION1.0	VERSION 1.0		VERSION 1.0
    ChromoSeg	Macintosh Classic (OS 9)	224 k	ChromoSegMac.sea (self-extracting archive with the program and two text files from which it reads in settings.)
    ChromoSeg	Windows	164 k	ChromoSegPC.sea (self-extracting archive with the program and two text files from which it reads in settings.)
    ChromoSeg	Source Code	216 k	Included in the tarball "EricCode.tgz" which also includes the source code for GFMCMC, NewHybrids, and Pedagog.
    ChromoSeg	Documentation		Coming soon

• GFMCMC (GLUT for Markov Chain Monte Carlo) This is a library of C code that I wrote to use the (relatively) platform-independent OpenGL Utilities Toolkit (GLUT) for rendering pictures of one's MCMC simulation in real time. It is essentially a small application programming interface. By writing a few functions that let GFMFC interface with the simulation program, GFMFC can take care of window management, Markov chain control, resetting of averages, etc., while the developer can write a few functions using OpenGL to render real-time images of the variables in his or her simulation.

  • Program	Platform/Description	Size	Download
    VERSION1.0	VERSION 1.0		VERSION 1.0
    GFMCMC	User's Guide	156 k	GFMCMC_UserGuide.pdf. This is a guide for USER's of finished programs. Not for developers.
    GFMCMC	Developer's Guide	124 k	Incomplete Draft---Still working on finishing up this documentation. You can get a flavor for things from this, though.
    GFMCMC	Source Code	216 k	Included in the tarball "EricCode.tgz" which also includes the source code for NewHybrids, ChromoSeg, and Pedagog.