Metadata-Version: 2.1
Name: orthohmm
Version: 0.0.0
Summary: HMM-based orthology
Home-page: https://github.com/jlsteenwyk/orthohmm
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering
Description-Content-Type: text/markdown
License-File: LICENSE.md

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OrthoHMM infers gene orthology using Hidden Markov Models.<br /><br />
If you found orthohmm useful, please cite *COMING SOON  *. Steenwyk et al. 2024, [JOURNAL]. doi: [DOI](https://jlsteenwyk.com/publication_pdfs/2020_Steenwyk_etal_PLOS_Biology.pdf).

---

<br />

This documentation covers downloading and installing OrthoHMM. Details about each function as well as tutorials for using OrthoHMM are available in the [online documentation](https://jlsteenwyk.com/OrthoHMM/).

<br />

**Quick Start**

```shell
# install
pip install orthohmm
# run
orthohmm <path_to_directory_of_FASTA_files>
```

<br />

**Installation**

**If you are having trouble installing OrthoHMM, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**

To install using *pip*, we recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
```shell
# create virtual environment
python -m venv venv
# activate virtual environment
source venv/bin/activate
# install orthohmm
pip install orthohmm
```
**Note, the virtual environment must be activated to use *orthohmm*.**

After using OrthoHMM, you may wish to deactivate your virtual environment and can do so using the following command:
```shell
# deactivate virtual environment
deactivate
```

<br />

Similarly, to install from source, we recommend using a virtual environment. To do so, use the following commands:
```shell
# download
git clone https://github.com/JLSteenwyk/orthohmm.git
cd orthohmm/
# create virtual environment
python -m venv venv
# activate virtual environment
source venv/bin/activate
# install
make install
```
To deactivate your virtual environment, use the following command:
```shell
# deactivate virtual environment
deactivate
```
**Note, the virtual environment must be activated to use *orthohmm*.**

<!-- <br />

To install via anaconda, execute the following command:

``` shell
conda install bioconda::orthohmm
```
Visit here for more information: https://anaconda.org/bioconda/orthohmm -->
