tutorial_blupf90.tex

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            pdfauthor={Yutaka Masuda},
            pdftitle={Introduction to BLUPF90 suite programs},
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\begin{document}

\frontmatter
\title{Introduction to BLUPF90 suite programs\\ Standard Edition (Ver 1.9.0)}
\author{Yutaka Masuda}
\date{August 2026}
\maketitle

\chapter{Revision History}
\input{history.tex}

\chapter{Acknowledgment}
\input{acknowledgment.tex}

\chapter{License}
\input{license.tex}

\tableofcontents

\mainmatter
%\input{blupf90.tex}
\chapter{Introduction}
\input{introduction_short.tex}
\input{introduction_difference.tex}
\input{introduction_condition.tex}
\input{introduction_plus.tex}
\input{introduction_about.tex}

\chapter{Download and Installation}
\input{installation_start.tex}
\input{installation_availability.tex}
\input{installation_windows.tex}
\input{installation_linux.tex}
\input{installation_env.tex}
\input{installation_editor.tex}

\chapter{Quick tour of BLUPF90}
\input{quicktour_start.tex}
\input{quicktour_fixed.tex}
\input{quicktour_mixed.tex}
\input{quicktour_ssgblup.tex}
\input{quicktour_mt.tex}

\chapter{Data preparation with RENUMF90}
\input{renum_start.tex}
\input{renum_basic.tex}
\input{renum_pedigree.tex}
\input{renum_genomic.tex}
\input{renum_mt.tex}
\input{renum_advanced.tex}
\input{renum_norenum.tex}

\chapter{Variance component estimation}
\input{vc_aireml.tex}
\input{vc_gs.tex}
\input{vc_advanced_aireml.tex}
\input{vc_advanced_gs.tex}

\chapter{Various models}
\input{mrode_start.tex}
\input{mrode_c04ex041_animal_model.tex}
\input{mrode_c04ex042_sire_model.tex}
\input{mrode_c04ex043_reduced_animal_model.tex}
\input{mrode_c04ex044_animal_model_with_groups.tex}
\input{mrode_c05ex051_repeatability_model.tex}
\input{mrode_c05ex052_common_environment.tex}
\input{mrode_c06ex061_mt_equal_design.tex}
\input{mrode_c06ex062_mt_missing.tex}
\input{mrode_c06ex063_mt_unequal_design.tex}
\input{mrode_c06ex064_mt_no_covariance.tex}
\input{mrode_c07ex071_canonical_transformation.tex}
\input{mrode_c07ex072_cholesky_transformation.tex}
\input{mrode_c08ex081_maternal.tex}
\input{mrode_c08ex082_reduced_maternal.tex}
\input{mrode_c09ex091_social_interaction.tex}
\input{mrode_c10ex101_fixed_regression.tex}
\input{mrode_c10ex102_random_regression.tex}
\input{mrode_c11ex111_fixed_snp.tex}
\input{mrode_c11ex112_mixed_snp.tex}
\input{mrode_c11ex113_gblup.tex}
\input{mrode_c11ex114_snp_solutions.tex}
\input{mrode_c11ex116_allele_frequency.tex}
\input{mrode_c11ex117_polygenic.tex}
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\input{mrode_c11ex1113_mt.tex}
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\input{mrode_c13ex131_dominance.tex}
\input{mrode_c13ex132_addtive_and_dominance.tex}
\input{mrode_c13ex133_genomic_dominance.tex}
\input{mrode_c13ex134_genomic_inbreeding.tex}
\input{mrode_c13ex135_epistasis.tex}
\input{mrode_c15ex151_threshold.tex}
\input{mrode_c15ex152_threshold_linear.tex}

\chapter{Large-scale genetic evaluation}
\input{largescale_start.tex}
\input{largescale_issues.tex}
\input{largescale_pcg.tex}
\input{largescale_reliability.tex}
\input{largescale_reml.tex}

\chapter{Practical genomic analysis}
\input{genomic_start.tex}
\input{genomic_overview.tex}
\input{genomic_files.tex}
\input{genomic_qc.tex}
\input{genomic_tuning.tex}
\input{genomic_ssgblup.tex}
\input{genomic_gblup.tex}
\input{genomic_gwas.tex}

\backmatter

\chapter{References}
\input{references.tex}

%\appendix
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\end{document}