AMPHORA

AMPHORA is a software tool developed to enable the analysis of large-scale protein phylogenetic inference. With the explosive growth of genomic data, there has been an increasing need for using protein markers in phylogenetic inference. However, the existing bottlenecks have limited the ability to carry out this type of analysis on a large scale. AMPHORA overcomes these bottlenecks by providing an automated pipeline for phylogenomic analysis.

One of the key strengths of AMPHORA is its ability to demonstrate high throughput capabilities. This is made possible by its efficient algorithms and optimized workflows. The tool has been used to construct a genome tree of 578 bacterial species, and it has also been used to assign phylotypes to 18,607 protein markers identified in metagenomic data collected from the Sargasso Sea.

AMPHORA has been designed with a user-friendly interface, making it easy to use for researchers without extensive computational backgrounds. It provides a comprehensive suite of tools for phylogenomic analysis, including multiple sequence alignment, phylogenetic inference, and tree visualization.