feat: added analysis of target presence over all taxonomic levels

[m-jahn]

• 1 new section
• 1 new figure

[Copilot]

Pull request overview

This pull request adds a new analysis section to the homology search pipeline that analyzes and visualizes target presence across taxonomic levels.

Changes:

• Added a new Python script source/plot_phylo_summary.py for creating stacked bar charts showing target presence across taxonomic ranks
• Extended the Jupyter notebook pipeline/homology_search.ipynb with a new section "Analyse presence in all bacterial taxa" that includes documentation and code cells for running the phylogenetic summary and plotting scripts
• Updated the HTML documentation docs/homology_search.html to reflect the notebook changes (auto-generated)

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
source/plot_phylo_summary.py	New script for plotting phylogenetic summary data as stacked bar charts with annotations
pipeline/homology_search.ipynb	Added new section with markdown documentation and code cells to run phylogenetic summary analysis and visualization
docs/homology_search.html	Auto-generated HTML documentation reflecting the notebook changes

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