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‎student-guide/docs/About.md‎

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# About the Authors {-}
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These credits are based on our [course contributors table guidelines](https://github.com/jhudsl/OTTR_Template/wiki/How-to-give-credits).
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|Credits|Names|
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|-------|-----|
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|**Pedagogy**||
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|Lead Content Instructor|Elizabeth Humphries|
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|Content Idea Contributor| [Ava Hoffman], [Frederick Tan]|
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|Content Directors | Elizabeth Humphries, [Jeff Leek], [Frederick Tan]|
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|**Production**||
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|Content Publisher|[Ira Gooding]|
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|**Technical**||
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|Template Publishing Engineers|[Candace Savonen], [Carrie Wright], [Ava Hoffman]|
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|Publishing Maintenance Engineer|[Candace Savonen]|
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|Technical Publishing Stylists|[Carrie Wright], [Candace Savonen]|
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|Package Developers ([ottrpal])|[John Muschelli], [Candace Savonen], [Carrie Wright]|
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|**Funding**||
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|Funder| [National Human Genome Research Institute (NHGRI)] |
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|Funding Staff| Fallon Bachman, Jennifer Vessio, Emily Voeglein|
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<!-- |Content Contributor | [Jeff Leek], [Michael Schatz], [Frederick Tan]| -->
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<!-- |Content Editors| [Katherine Cox], Natalie Kucher, [Frederick Tan]| -->
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<!-- |Content Directors | Kasper Hansen, [Jeff Leek], [Frederick Tan]| -->
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<!-- |Content Consultants (General) | [Jeff Leek], [Frederick Tan], [Carrie Wright] | -->
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```
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## ─ Session info ───────────────────────────────────────────────────────────────
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## setting value
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## version R version 4.3.2 (2023-10-31)
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## os Ubuntu 22.04.4 LTS
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## system x86_64, linux-gnu
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## ui X11
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## language (EN)
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## collate en_US.UTF-8
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## ctype en_US.UTF-8
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## tz Etc/UTC
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## date 2025-05-06
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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##
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## package * version date (UTC) lib source
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## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2)
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## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0)
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## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0)
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## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0)
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## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0)
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## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0)
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## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0)
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## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0)
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## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0)
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## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0)
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## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0)
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## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0)
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## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0)
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## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2)
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## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0)
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## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0)
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## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0)
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## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0)
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## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0)
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## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0)
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## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0)
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## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0)
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## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0)
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## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0)
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## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0)
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## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0)
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## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0)
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## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0)
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## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2)
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## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0)
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## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0)
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## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0)
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## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0)
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## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0)
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## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0)
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## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0)
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## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0)
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## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2)
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## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0)
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## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0)
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##
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## [1] /usr/local/lib/R/site-library
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## [2] /usr/local/lib/R/library
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##
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## ──────────────────────────────────────────────────────────────────────────────
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```
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<!-- Author information -->
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[Katherine Cox]: https://publichealth.jhu.edu/faculty/4170/katherine-cox
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[Ira Gooding]: https://publichealth.jhu.edu/faculty/4130/ira-gooding
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[Ava Hoffman]: https://www.avahoffman.com/
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[Jeff Leek]: https://jtleek.com/
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[John Muschelli]: https://johnmuschelli.com/
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[National Human Genome Research Institute (NHGRI)]: https://www.genome.gov/
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[Candace Savonen]: https://www.cansavvy.com/
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[Michael Schatz]: http://schatz-lab.org/
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[Frederick Tan]: https://carnegiescience.edu/frederick-tan
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[Carrie Wright]: https://carriewright11.github.io/
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<!-- Links -->
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[Ottrpal]: https://github.com/jhudsl/ottrpal
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<!-- Fill out this table using these instructions: https://github.com/jhudsl/DaSL_Course_Template_Bookdown/wiki/How-to-give-credits
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For JHU courses, You will need to add Ira as a credit:
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|Content Publisher|[Ira Gooding]|
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...
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[Ira Gooding]: https://publichealth.jhu.edu/faculty/4130/ira-gooding
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-->
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2022 GitHub, Inc.
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Terms
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Privacy
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Security
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Status
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Doc

‎student-guide/docs/References.md‎

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# References

‎student-guide/docs/Student_Guide.docx‎

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‎student-guide/docs/index.md‎

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---
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title: "Molecular Phylogenetic Techniques"
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date: "May 06, 2025"
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site: bookdown::bookdown_site
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documentclass: book
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bibliography: book.bib
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biblio-style: apalike
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link-citations: yes
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description: Description about Course/Book.
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favicon: assets/AnVIL_style/anvil_favicon.ico
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---
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# About this Book {-}
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This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063).
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## Skills Level {-}
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::: {.notice}
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_Genetics_
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<!-- **Novice**: no genetics knowledge needed -->
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_Programming skills_
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<!-- **Novice**: no programming experience needed -->
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:::
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## AnVIL Collection {-}
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Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/

‎student-guide/docs/reference-keys.txt‎

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student-guide
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activity-one
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activity-two
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references

‎student-guide/docs/student-guide.md‎

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# Student Guide
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## Activity One
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Many of the AnVIL books that are designed for teaching a class or workshop contain information aimed at the instructor.
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You might want to create a "student guide" that contains a different subset of Rmd files from your book, or renders to a different output format (e.g. word document). You can specify the output and Rmd files that will be used for the student guide using the `_output.yml` and `_bookdown.yml` files in the `student-guide` directory.
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By default, repositories based on `AnVIL_Template` create a docx file containing this chapter as an example. Once you have adjusted `student-guide/bookdown.yml` to include the chapters you want in your student guide, you can link to it by replacing `{repo-name}` in the following URL:
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`https://github.com/jhudsl/{repo-name}/raw/main/student-guide/docs/Student_Guide.docx`
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When someone clicks this link, they will download the docx file. For example, here is the link for the student guide from `AnVIL_Template`:
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https://github.com/jhudsl/AnVIL_Template/raw/main/student-guide/docs/Student_Guide.docx
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## Activity Two
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Steps of the guide could go here.

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