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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 57920669e12271a6a163c439c16557c9
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/docs/biblio.doctree b/.doctrees/docs/biblio.doctree
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+pypop.org
diff --git a/PyPopLinux-0.7.0.tar.gz b/PyPopLinux-0.7.0.tar.gz
diff --git a/PyPopWin32-0.7.0.zip b/PyPopWin32-0.7.0.zip
diff --git a/_sources/docs/biblio.rst.txt b/_sources/docs/biblio.rst.txt
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+.. raw:: latex
+
+   \cleardoublepage
+   \begingroup
+   \renewcommand\chapter[1]{\endgroup}
+   \phantomsection
+
+.. _refs:
+
+**********
+References
+**********
+
+.. bibliography::
+
+..
+   [Cano:etal:2007] Pedro Cano. 2007. “Common and well-documented HLA
+   		    alleles: report of the ad-hoc committee of the American Society
+   		    for Histocompatiblity and Immunogenetics”. 68. 5. 392-417.
+   		    \ *Human Immunology*.
+   
+   [Chen:etal:1999] JJ Chen, JA Hollenbach, EA Trachtenberg, JJ Just,
+   		    M Carrington, KS Ronningen, A Begovich, MC King, SK McWeeney, SJ
+   		    Mack, HA Erlich, and G Thomson. 1999. “Hardy-Weinberg testing for
+   		    HLA class II (DRB1, DQA1, DQB1 and DPB1) loci in 26 human ethnic
+   		    groups”. 54. 533-542. \ *Tissue Antigens*.
+   
+   [Cramer:1946] H Cramer. \ *Mathematical Models of Statistics*.
+   		 1946. Princeton University Press. Princeton NJ.
+   
+   [Dempster:1977] A Dempster, N Laird, and D Rubin. 1977. “Maximum
+   		   likelihood estimation from incomplete data using the EM
+   		   algorithm”. 39. 1-38. \ *J Royal Stat Soc*.
+   
+   [Ewens:1972] W Ewens. 1972. “The sampling theory of selectively
+   		neutral alleles.”. \ *Theor. Pop. Biol*. 3. 87-112.
+   
+   [Excoffier:Slatkin:1995] Laurent Excoffier and Montgomery Slatkin.
+   			    1995. “Maximum-likelihood estimation of molecular haplotype
+   			    frequencies in a diploid population”. \ *Molecular Biology and
+   			    Evolution*. 12. 5. 921-927.
+   
+   [Guo:Thompson:1992] S W Guo and E A Thompson. 1992. “Performing
+   		       the exact test of Hardy-Weinberg proportion for multiple alleles”.
+   		       \ *Biometrics*. 48. 361-72.
+   
+   [Hedrick:1987] P W Hedrick. 1987. “Gametic disequilibrium
+   		  measures: proceed with caution”. 117. 2. 331-41. \ *Genetics*.
+   
+   [Lancaster:etal:2003] Alex Lancaster, Mark P Nelson, Richard M
+   			 Single, Diogo Meyer, and Glenys Thomson. 2003. “PyPop: a software
+   			 framework for population genomics: analyzing large-scale
+   			 multi-locus genotype data”. \ *Pacific Symposium on Biocomputing*.
+   			 R B Altman. et al.. vol 8. 514-525. \ 
+   			 .. [:download:`PDF </html_root/psb-pypop.pdf>` (344 kB)].
+   
+   [Lancaster:etal:2007a] Alex Lancaster, Mark P Nelson, Richard M
+   			  Single, Diogo Meyer, and Glenys Thomson. 2007a. \ *Software
+   			  framework for Biostatistics Core*. JA Hansen. \ *Immunobiology of
+   			  the Human MHC: Proceedings of the 13th International
+   			  Histocompatibility Workshop and Conference*. IHWG Press. Seattle,
+   			  Washington. I. 510-517.
+   
+   [Lancaster:etal:2007b] Alex Lancaster, Richard M Single, Owen D
+   			  Solberg, Mark P Nelson, and Glenys Thomson. 2007b. “PyPop update -
+   			  a software pipeline for large-scale multilocus population
+   			  genomics.”. \ *Tissue Antigens*. 69 Suppl 1. 192-197.
+   			  .. [:download:`PDF </html_root/tissue-antigens-lancaster-2007.pdf>`
+   			  (150 kB)].
+   
+   [Mack:etal:2007] Steven J. Mack, Alicia Sanchez-Mazas, Diogo
+   		    Meyer, Richard M Single, Yingssu Tsai, and Henry Erlich. 2007.
+   		    \ *Methods used in the generation and preparation of data for
+   		    analysis in the 13th International Histocompatibility Workshop*.
+   		    JA Hansen. \ *Immunobiology of the Human MHC: Proceedings of the
+   		    13th International Histocompatibility Workshop and Conference*.
+   		    IHWG Press. Seattle, Washington. I. 564-579.
+   
+   [Meyer:etal:2007] Diogo Meyer, Richard M Single, Steven J. Mack,
+   		     Alex Lancaster, Mark P Nelson, M. Fernánndez-Viñaa, Henry Erlich,
+   		     and Glenys Thomson. 2007. \ *Haplotype frequencies and linkage
+   		     disequilibrium among classical HLA genes*. JA Hansen.
+   		     \ *Immunobiology of the Human MHC: Proceedings of the 13th
+   		     International Histocompatibility Workshop and Conference*. IHWG
+   		     Press. Seattle, Washington. I. 705-746.
+   
+   [Salamon:etal:1999] H Salamon, W Klitz, S Easteal, X Gao, HA
+   		       Erlich, M Fernandez-Vina, and EA Trachtenberg. 1999. “Evolution of
+   		       HLA class II molecules: Allelic and amino acid site variability
+   		       across populations”. 152. 393-400. \ *Genetics*.
+   
+   [Schneider:etal:2000] S Schneider, D Roessli, and L Excoffier.
+   			 2000. “Arlequin: A software for population genetics data analysis.
+   			 http://lgb.unige.ch/arlequin/”. Ver 2.000. Genetics and Biometry
+   			 Lab, Dept. of Anthropology, University of Geneva.
+   
+   [Single:etal:2007a] RM Single, D Meyer, and G Thomson. 2007a.
+   		       \ *Statistical methods for analysis of population genetic data*.
+   		       JA Hansen. \ *Immunobiology of the Human MHC: Proceedings of the
+   		       13th International Histocompatibility Workshop and Conference*.
+   		       IHWG Press. Seattle, Washington. I. 518-522.
+   
+   [Slatkin:1994] M Slatkin. 1994. “An exact test for neutrality
+   		  based on the Ewens sampling distribution”. \ *Genetical Research*.
+   		  64. 71-74.
+   
+   [Slatkin:1996] M Slatkin. 1996. “A correction to the exact test
+   		  based on the Ewens sampling distribution”. \ *Genetical Research*.
+   		  68. 259-260.
+   
+   [Solberg:etal:2008] Owen D. Solberg, Steven J. Mack, Alex K. Lancaster,
+   		       Richard M. Single, Yingssu Tsai, Alicia Sanchez-Mazas, and Glenys
+   		       Thomson Hum Immunol (2008), doi: 10.1016/j.humimm.2008.05.001
+   
+   [Thomson:Single:2014] Glenys Thomson and Richard M. Single. 2014.
+                         “Conditional Asymmetric Linkage Disequilibrium (ALD): Extending the 
+                         Biallelic r2 Measure” \ *Genetics*, 198, 321–331.
+   
+   [Watterson:1978] G Watterson. 1978. “The homozygosity test of
+   		    neutrality”. \ *Genetics*. 88. 405-417.
+   
+.. 		    
+   AB Begovich GR McClure VC Suraj RC Helmuth N Fildes TL Bugawan HA Erlich 1992 Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. 148 249-58 J Immunol
+   AM Valdes G Thomson 1997 Detecting disease-predisposing variants: The haplotype method 60 703-716 American Journal of Human Genetics
+   AM Valdes SK McWeeney D Meyer MP Nelson G Thomson 1999 Locus and population specific evolution in HLA class II genes 63 27-43 Annals of Human Genetics
+   AS Dienard KK Kidd 1995 Levels of DNA polymorphism in extant and extinct hominoids. In:The Origin and Past of Modern Humans as Viewed from DNA. 149-170 S Brenner K Hanihara World Scientific New Jersey
+   Bray Tim Jean Paoli C M Sperberg-McQueen Eve Maler 2000 `Extensible Markup Language 1.0 (XML) <http://www.w3.org/TR/REC-xml/>`__ Second Edition World Wide Web Consortium
+   D A Rhodes J Trowsdale 1999 Genetics and molecular genetics of the MHC Rev. Immunogenetics 1 1 21-31
+   D Fallin NJ Schork 2000 Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data 67 947-959 Am J Hum Genet
+   D Hartl A Clark Principles of Population Genetics Third Edition Sinauer Sunderland MA
+   D M Beazley 1996 SWIG: an easy to use tool for integrating scripting languages with C and C++, available at http://www.swig.org/ 4th Annual Tcl/Tk Workshop '96 USENIX July 10-13, 1996 129-139
+   D Meyer G Thomson 2001 How selection shapes variation of the human major histocompatibility complex: a review 65 1-26 Annals of Human Genetics
+   D.E Reich M Cargill S Bolk J Ireland P C Sabeti D J Richter T Lavery R Kouyoumjian S F Farhadian R Ward E S Lander Linkage disequilibrium in the human genome 2001 411 199-204 Nature
+   E Louis ER Dempster 1987 An exact test for Hardy-Weinberg and multiple alleles. 43 805-812 Biometrics
+   F Yates 1934 Contingency tables involving small numbers and the Chi-square test 1 217-235 (supp) J Royal Stat Soc
+   G Thomson 1977 The effect of a selected locus on linked neutral loci Genetics 85 753-788
+   G Thomson W Klitz 1987 Disequilibrium pattern analysis. I. Theory Genetics 116 623-632
+   G van Rossum F L Drake 2001 Python Reference Manual, available at http://www.python.org/ PythonLabs Virginia
+   GA Huttley MW Smith M Carrington SJ O'Brien 1999 A scan for linkage disequilibrium across the human genome 152 1711-22 Genetics
+   GNOME Project http://www.gnome.org/
+   GNU General Public License http://www.gnu.org/licenses/gpl.html Free Software Foundation Boston MA
+   H Levene 1949 On a matching problem arising in genetics. 20 627-642 Ann Math Stat
+   IMGT/HLA Database http://www.ebi.ac.uk/imgt/hla/
+   J Felsenstein 1989 PHYLIP Phylogeny Inference Package (Version 3.2) http://evolution.genetics.washington.edu/phylip.html Cladistics 5 164-166
+   J Robinson M Waller P Parham N de Groot R Bontrop LJ Kennedy P Stoehr SGE Marsh 2007 2003 IMGT/HLA and IMGT/MHC - Sequence Databases for the study of the Major Histocompatibility Complex HLA2007
+   JA Hollenbach G Thomson K Cao M Fernandez-Vina HA Erlich TL Bugawan C Winkler M Winter W Klitz 2001 HLA diversity, differentiation, and haplotype evolution in Mesoamerican natives 62 378-390 Human Immunology
+   JC Long RC Williams M Urbanek 1995 An E-M algorithm and testing strategy for multiple-locus haplotypes 56 799-810 Am J Hum Genet
+   JJ Chen G Thomson 1999 55 1269-72
+   James Clark 1999 `Extensible Stylesheet Language Transformations 1.0 (XSLT) <http://www.w3.org/TR/xslt/>`__ World Wide Web Consortium
+   L F Barcellos G Thomson M Carrington J Schafer A B Begovich P Lin X H Xu 1997 Chromosome 19 single-locus and multilocus haplotype associations with multiple sclerosis. Evidence of a new susceptibility locus in Caucasian and Chinese patients 278 1256-61 Jama
+   L F Barcellos W Klitz L L Field R Tobias A M Bowcock R Wilson Nelson M P 1997 Association mapping of disease loci, by use of a pooled DNA genomic screen 61 734-47 Am J Hum Genet
+   M Baur J Danilovs 1980 Population genetic analysis of HLA-A, B, C, DR, and other genetic markers. P Terasaki Histocompatibility Testing UCLA Tissue Typing Laboratory Los Angeles 955-993
+   M Hawley K Kidd 1995 HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes 86 409-411 Journal of Heredity
+   M Raymond F Rousset 1995 GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism, available from ftp://ftp.cefe.cnrs-mop.fr/genepop J. Hered 86 248-249
+   M.J Daly J.D Rioux S.E Schaeffer T.J Hudson E.S Lander 2001 High-resolution haplotype structure in the human genome 29 229-232 Nature Genetics
+   N Metropolis R AW AH Teller T E 1953 Equations of state calculations by fast computing machines. 21 1087-1092 Journal of Chemical Physics
+   Open Source Initiative https://opensource.org/
+   P F Dubois K Hinsen J Hugunin 1996 Numerical Python, available at https://numpy.sf.net/ Computers in Physics 10 3 262-267
+   P Hedrick G Thomson 1983 Evidence for balancing selection at HLA 104 449-456 Genetics
+   P Hedrick Genetics of Populations 1999 Second Edition Jones and Bartlett Sunbury MA
+   PV Moonsamy W Klitz MG Tilanus AB Begovich 1997 Genetic variability and
+   R Elston R Forthofer 1977 Testing for Hardy-Weinberg equilibrium in small samples 33 536-542 Biometrics
+   R M Single D Meyer J A Hollenbach M P Nelson J A Noble H A Erich G Thomson 2002 Haplotype frequency estimation in patient populations: the effect of departures from Hardy-Weinberg proportions and collapsing over a locus in the HLA region 22 186-195 Genetic Epidemiology
+   RF Schipper J D'Amaro P de Lange GM Schreuder JJ van Rood M Oudshoorn 1998 Validation of haplotype frequency estimation methods 59 518-523 Hum Immunol
+   RM Single D Meyer Steven J. Mack Alex Lancaster Mark P Nelson M. Fernánndez-Viñaa Henry Erlich G Thomson 2007b Single locus polymorphism of classical HLA genes. HLA2007 I 653-704
+   Ross Ihaka Robert Gentleman R: A Language for Data Analysis and Graphics https://www.r-project.org/ 1996 Journal of Computational and Graphical Statistics 5 3 299-314
+   T Emigh 1980 A comparison of tests for Hardy-Weinberg equilibrium 36 627-642 Biometrics
+   W Cochran 1954 Some methods for strengthening the common Chi-Squared tests 10 417-451 Biometrics
+   WP Robinson MA Asmussen G Thomson 1991 Three-locus systems impose additional constraints on pairwise disequilibria Genetics 129 925-30
+   dbMHC https://www.ncbi.nlm.nih.gov/IEB/Research/GVWG/MHC/
+   libxslt, XSLT C library for GNOME https://xmlsoft.org/
+   linkage disequilibrium within the DP region in the CEPH families 58 112-121 Hum Immunol
diff --git a/_sources/docs/guide-chapter-changes.rst.txt b/_sources/docs/guide-chapter-changes.rst.txt
@@ -0,0 +1,14 @@
+.. _guide-changes-authors:
+
+*******************
+Authors and history 
+*******************
+
+.. include:: ../../AUTHORS.rst
+
+PyPop Release History
+=====================
+
+.. include:: ../../NEWS.md
+   :parser: myst_parser.sphinx_
+   :start-after: https://semver.org).
diff --git a/_sources/docs/guide-chapter-contributing.rst.txt b/_sources/docs/guide-chapter-contributing.rst.txt
@@ -0,0 +1,7 @@
+*********************
+Contributing to PyPop
+*********************
+
+.. include:: ../../CONTRIBUTING.rst
+   :start-after: guide-contributing-start:
+
diff --git a/_sources/docs/guide-chapter-install.rst.txt b/_sources/docs/guide-chapter-install.rst.txt
@@ -0,0 +1,7 @@
+****************
+Installing PyPop
+****************
+
+.. include:: ../../README.rst
+   :start-after: guide-include-start:
+   :end-before: guide-include-end: