Poplars

Poplars is a collection of open-source implementations of popular tools from Los Alamos National Laboratory HIV Sequence Database (LANL), which is an important web resource for researchers in HIV/AIDS that curates published sequence data and online tools for processing these data. Los Álamos is "the cottonwoods" in Spanish [source], and cottonwoods are a common name for poplars.

Available Tools

Implementations of the following tools are currently available:

• Hypermut
• Rip-like
• Sequence locator

Dependencies

Python Requiremnts

Poplars requires SciPy.

Poplars was tested using Python 3.6.x and Python 2.7x and is compatible with all major versions of Python.

Poplars uses MAFFT (Multiple Alignment using Fast Fourier Transform) for sequence alignment, so for ease of use we have distributed all-in-one MAFFT packages for Linux (MAFFT Version 7.427), Windows (MAFFT Version 7.429), and Mac OS X (MAFFT 7.427).

Operating System Requirements

Poplars is compatible with:

• Windows 10
• Linux
• Mac OS X (Mac OS X 10.5-10.14, x86 only)

Poplars was tested on Windows 10 Version 1903, Ubuntu 18.04.2, and Mac OS X Mavericks.

Installation

Poplars can be installed directly from the source code on GitHub or through the Python Package Index pip.

From Source

1. Navigate to your directory of choice. Then clone the Poplars repository by running the following command in your terminal:

   git clone https://github.com/PoonLab/Poplars.git
   

   Alternatively, you can download Poplars into your directory of choice.

2. After downloading or cloning the repository, a directory called Poplars will be created in your working directory. Navigate to the Poplars folder and run setup.py in your terminal using one of the following commands:

   sudo python setup.py install 
   

   or

   sudo python3 setup.py install
   

   setup.py will install Poplars along with MAFFT binaries (executables) that are specific to your machine.

   Poplars will be installed into your Python site-packages (so you can use Poplars anywhere you can use Python!)

Using pip

1. To install Poplars, run the following command in your terminal:

   pip install poplars
   

2. To upgrade the version of Poplars run the following command in your terminal:

   pip install --upgrade poplars
   

3. To uninstall Poplars run the following command in your terminal:

   pip uninstall poplars
   

For more detailed installation instructions, please refer to INSTALL.md