phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison.

Phylogenetic reconstruction is a multi-step process that typically involves sequence retrieval, alignment, trimming, and tree inference, often requiring the integration of multiple independent tools. This fragmented workflow increases technical complexity and limits reproducibility, particularly in large-scale analyses. Here, we present phyloPipeR, an R package that provides an integrated and automated framework for end-to-end phylogenetic analysis and tree comparison within a unified environment. The phyloPipeR enables complete workflows from ortholog retrieval to tree inference and quantitative comparison, while also supporting modular execution of individual steps. The package implements multiple phylogenetic inference methods and supports both concatenation and coalescent strategies for multi-gene analyses. By integrating tree reconstruction and quantitative comparison within a single framework, phyloPipeR improves reproducibility, reduces technical barriers, and provides a scalable solution for systematic and integrative evolutionary studies.