https://github.com/pblischak/evol2017
Tutorial, code, and data for Evolution 2017
https://github.com/pblischak/evol2017
hybridization jupyter-notebook python27 tutorial
Last synced: 11 months ago
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Tutorial, code, and data for Evolution 2017
- Host: GitHub
- URL: https://github.com/pblischak/evol2017
- Owner: pblischak
- Created: 2017-06-20T13:58:44.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-06-26T18:20:01.000Z (almost 9 years ago)
- Last Synced: 2025-02-17T07:44:48.828Z (about 1 year ago)
- Topics: hybridization, jupyter-notebook, python27, tutorial
- Language: Jupyter Notebook
- Size: 1.39 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## Materials for Evolution 2017
> **NB**: Simulating new data sets and analyzing any of the data files requires
> a few pieces of software. To simulate new data sets using the code provided in the
> tutorial, you will need [`ms`](http://home.uchicago.edu/rhudson1/source/mksamples.html)
> and [`Seq-Gen`](http://tree.bio.ed.ac.uk/software/seqgen/). To analyze the data sets and
> any of the results files you will need to install [**HyDe**](http://hybridization-detection.rtfd.io).
### HyDe Tutorial
The file `HyDe.ipynb` is a Jupyter Notebook with a walkthrough of the analyses
that we conducted as part of our talks at Evolution.
### Data Files
- `data.txt` and `map.txt`: these are simulated data sets that ca be during these
the tutorial to test out the different features of HyDe. The code to generate
them is in the `HyDe.ipynb` notebook.
- `heliconius-out.txt` and `heliconius-boot.txt`: these are the results files from
our analysis of the _Heliconius_ data set from Martin _et al_. (2013).
- `swordtail-out.txt`: this is the result file from our analysis of the swordtail
data set from Cui _et al_ (2013).