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README.md

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# TreeProfiler Overview
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TreeProfiler is a command line tool designed to automate the annotation of large phylogenetic trees with corresponding metadata. It also facilitates the visual exploration of these annotations as phylogenetic profiles, making it a powerful resource for researchers working with complex biological data.
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![treeprofiler abstract](https://github.com/dengzq1234/treeprofiler_gallery/blob/main/TreeProfiler_2025.png?raw=true)
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## Graphical Abstract
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<img src="https://github.com/dengzq1234/treeprofiler_gallery/blob/main/TreeProfiler_2025.png?raw=true" alt="TreeProfiler Abstract" width="640" height="360" />
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Key Features:
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## Key Features:
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- Automated Annotation that integrates metadata into phylogenetic tree, and summarizes annotation in internal nodes, including:
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- Categorical/Numerical metadata in TSV/CSV format
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- Taxonomic Annotation of NCBI/GTDB taxonomy database
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- Phylogenetic Signal Delta Statistic]
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- Lineage Specificity Analysis
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## Demo Video
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<video width="640" height="360" controls>
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<source src="https://github.com/dengzq1234/treeprofiler_gallery/raw/refs/heads/main/motus_habitat_full_render.mp4" type="video/mp4">
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Your browser does not support the video tag.
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</video>
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## Documentation and Citation
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The official documentation of TreeProfiler is in https://dengzq1234.github.io/TreeProfiler/ where provides detailed instructions with examples.
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If you have any doubts, please drop a line in issue or contact https://x.com/deng_ziqi

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