Version 1.0.0

Highlights

• First public release of PhyloSOLID, rebuilt from the PhyloMosaicGenie prototype.
• Streamlined genotyping and phylogenetic analysis workflow.
• Improved code structure and reproducibility.
• Support for both scRNA-seq and scDNA-seq data.

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Features

• Dual-mode support: Works with both scRNA-seq and scDNA-seq data.
• Eight-step modular pipeline: From data loading and feature extraction to tree building and visualization.
• Mutation filtering: Built-in filters for quality control, including mappability, gnomAD, and RNA editing site filtering.
• Phylogenetic tree building: Generates Newick format trees from single-cell mutation data.
• Visualization outputs: Includes heatmaps, Circos plots, and tree visualizations.
• Flexible execution: Supports running individual steps or full pipeline with parallel processing support.

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Notes

• For usage details, see the docs site: https://github.com/douymLab/PhyloSOLID/