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Update README.md
idoerg Sep 15, 2017
82d70c8
Merge branch 'master' of https://github.com/nguyenngochuy91/Ancestral…
idoerg Mar 12, 2018
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19 changes: 19 additions & 0 deletions README.md
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Expand Up @@ -9,6 +9,17 @@ ROAGUE accepts a set of species and a gene block in a reference species. It then
ancestral states.

## Requirements
<<<<<<< HEAD
* Python 2.7.6+
* [Biopython >=1.63](Biopython)
* [http://www.drive5.com/muscle/downloads.htm](MUSCLE)
* ncbi-tools (ncbi-tools-bin)
* BLAST2 (blast2)
* BLAST+ (ncbi-blast+)
* [http://etetoolkit.org/](ete3)
install python-biopython muscle nscbi-tools-bin blast2 ete3
```
=======
* [Conda](https://conda.io/miniconda.html) (package manager so we don't have to use sudo)
* [Python 3+](https://www.python.org/download/releases/3.0/)
* [Biopython 1.63+](http://biopython.org/wiki/Download)
Expand All @@ -18,16 +29,24 @@ ancestral states.
* [ETE3](http://etetoolkit.org/download/) (python framework for tree)
* [PDA](http://www.cibiv.at/software/pda/#download) (optional if you want to debias your tree base on Phylogenetic Diversity)

>>>>>>> 6c29b90be7b41c3b164f0449dfe372ba05b241e2
## Installation
Users can either use github interface Download or type the following command in command line:
```bash
git clone https://github.com/nguyenngochuy91/Ancestral-Blocks-Reconstruction
```
Install Miniconda (you can either export path everytime you use roague, or add it the bashrc file)
```bash
<<<<<<< HEAD
sudo apt-get install python-biopython ncbi-tools-bin blast2 ncbi-blast+ muscle
```

For ete3, check installation instructions on this website: http://etetoolkit.org/download/
=======
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
export PATH=~/anaconda_ete/bin:$PATH;
>>>>>>> 6c29b90be7b41c3b164f0449dfe372ba05b241e2

```

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