# Poplar: a phylogenomics pipeline

## TL;DR

Poplar is a new computational pipeline that simplifies and speeds up the process of generating phylogenomic trees from genomic data.

## Contribution

Poplar introduces a streamlined, automated pipeline for phylogenomic analysis that requires no external databases and supports parallel computing.

## Key findings

- Poplar generates phylogenomic trees that closely match state-of-the-art published trees.
- The pipeline simplifies and accelerates phylogenomic analysis compared to manual methods.
- Poplar supports parallel execution for clusters and cloud computing.

## Abstract

Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist.

We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline.

Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.