bgc


Version 1.0 of bgc was released on 19 February 2012. See changelog below.

bgc  implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. The basic models implemented in bgc are described in detail in Gompert & Buerkle 2011, Gompert et al. 2012, and Gompert et al. 2012. Use of the software will require good familiarity with the models described in these papers. The software is described and evaluated in Gompert & Buerkle 2012b. Some programming might be required to generate input files.

  • Gompert Z, Buerkle CA (2011) Bayesian estimation of genomic clines. Molecular Ecology, 20:2111-2127. (article)
  • Gompert Z, Parchman TL, Buerkle CA. (2012) Genomics of isolation in hybrids. Philosophical Transactions of the Royal Society B: Biological Sciences, 1587:439-450. (article)
  • Gompert Z, Lucas LK, Nice CC, Fordyce JA, Forister ML, Buerkle CA (2012) Genomic  regions with a history of divergent selection affect fitness of hybrids between two butterfly species. Evolution, 66:2167–2181. (article)
  • Gompert Z, Buerkle CA (2012) bgc: Software for Bayesian estimation of genomic clines. Molecular Ecology Resources, doi: 10.1111/1755-0998.12009.x. (article)

Downloading and installation

We distribute bgc as source code that can be compiled by the user on any linux or UNIX platform. The compressed archive contains the source code for bgc, the source code for a auxiliary program to summarise MCMC output stored in HDF5 format, a software manual and a sample data set. The software manual can also be downloaded separately.

1. bgc 1.03 source code with examples and manual (bgcdist1.03.tar.gz)

2. bgc 1.03 software manual (manual)

bgc depends on the prior installation of the free and open-source GNU Scientific Library and HDF5. Instructions for compiling the software from source code are given in the software manual.

Questions and feedback

We have tested bgc with many simulated and empirical data sets on Mac OS X and linux computers. If you encounter problems that you think are associated with an error in the code, please let us know. We welcome your feedback and will do what we can to assist you with the software.

If you have a question, a feature request, or encounter a bug, please consult the manual for bgc, the manuscript that describes the models and thoroughly investigate your concern or problem. If you are interested in a new feature, we encourage you to consider writing it and contributing it as a proposed change or addition. If our assistance is required, please post a comment here and provide as much information as possible. Over time we will likely build a FAQ.

Changelog

  • 1.01 (15 August 2012) relative to 1.00
  1. The default for the -s option (sum-to-zero constraint on the cline parameters) is now 1 (TRUE) consistent with the manual (the default was 0).
  2. The quantile estimates for the first locus in the hdf5 file were incorrect and often negative. This error has been corrected.
  3. A bug that caused the program to occasionally crash when writing text output has been corrected. 
  • 1.02 (9 April 2013) relative to 1.01
    1. A bug that caused the program to crash when multiple admixed populations were analyzed simultaneously was corrected.      
  • 1.03 (3 April 2014) relative to 1.02
  1. The -F command line option can now be used to rename the ASCII text files and HDF5 file.

Terms of use

bgc is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

bgc is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Grant support for work

This material is based upon work supported by the National Science Foundation under Grant Nos. 0701757 (Plant Genome Research Program), 1011173 (Doctoral Dissertation Improvement Grant), and 1050149 (Evolutionary Processes) . Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF).


Subpages (2): FAQ Questions and comments
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Zach Gompert,
Apr 13, 2012, 1:10 PM
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bgcdist1.0.tar.gz
(1633k)
Zach Gompert,
Apr 13, 2012, 1:10 PM
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bgcdist1.01.tar.gz
(1632k)
Zach Gompert,
Aug 15, 2012, 5:54 PM
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bgcdist1.02.tar.gz
(5436k)
Zach Gompert,
Feb 3, 2014, 10:31 AM
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bgcdist1.03.tar.gz
(1860k)
Zach Gompert,
Apr 3, 2014, 11:26 AM
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Zach Gompert,
Feb 9, 2012, 11:05 AM
Ċ
Zach Gompert,
Feb 9, 2012, 10:34 AM
Ċ
Zach Gompert,
Feb 9, 2012, 11:11 AM
Ċ
Zach Gompert,
Oct 7, 2012, 11:42 AM
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