Uphyloplot2

Uphyloplot2 is a software tool to streamline the process of generating phylogenetic plots, particularly for depicting tumor clonality through the analysis of chromosome copy number variations (CNVs) inferred from single-cell RNA sequencing (scRNA-seq) data and other RNA-seq sources. Recent advancements in single-cell sequencing technologies have significantly enhanced the resolution at which tumor clonality and sub-clonal structures can be assessed, primarily by identifying CNVs. While single-cell DNA sequencing is a direct method for determining tumor sub-clones, it is often expensive and produces limited data compared to scRNA-seq methods. Recognizing this, several tools, including inferCNV, CaSpER, and HoneyBADGER, have been developed to infer CNV data from scRNA-seq and bulk RNA-seq data.

Previously, the visualization of tumor clonality using phylogenetic plots based on CNV data required manual analysis, which was time-consuming and prone to errors. Uphyloplot2 addresses this challenge by providing a Python script that automates the generation of phylogenetic plots from inferred RNA-seq data or any Newick formatted dendrogram file. This capability makes it significantly easier for researchers to visualize and interpret the complex relationships between different tumor sub-clones, enhancing our understanding of tumor heterogeneity and evolution.