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tli14 committed Dec 1, 2021
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Expand Up @@ -10,5 +10,5 @@ This repository provides codes and files to reproduce data and figures from the
* [Fasttree](http://www.microbesonline.org/fasttree/): Phylogenetic tree construction.
## Data
* The entire data generated in this study is too large to store on Github, some example data for _`Escherichia coli`_ are available [online](https://bcb.unl.edu/PanMAGs/) for testing MAG simulation, generating mixed MAG datasets, extracting and comparing core genes, and evaluating downstream analysis.
* [`Anaconda`](https://www.anaconda.com/) is used to create conda environment to run Python scripts, the required package `list` can be downloaded.
* [`Anaconda`](https://www.anaconda.com/) is used to create conda environment to run Python scripts, the required package [conda_list](https://github.com/tli14/PanMAGs/blob/main/conda_list) can be downloaded using ```conda create --name <env> --file conda_list```.
* Information about R packages needed to run R codes can be found in [R_packages](https://github.com/tli14/PanMAGs/blob/main/R_packages).

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