LZGraphs 2.3.1__tar.gz → 3.0.1__tar.gz

{lzgraphs-2.3.1 → lzgraphs-3.0.1}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Tom Chen (tomchen.org)
+Copyright (c) 2021-2026 Thomas Konstantinovsky
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

lzgraphs-3.0.1/MANIFEST.in

@@ -0,0 +1,7 @@
+include pyproject.toml
+include *.md
+include LICENSE
+include Makefile
+recursive-include include *.h
+recursive-include lib *.c
+recursive-include src/LZGraphs *.c

lzgraphs-3.0.1/Makefile

@@ -0,0 +1,125 @@
+CC      = gcc
+CFLAGS  = -O2 -Wall -Wextra -std=c11 -Iinclude
+LDFLAGS = -lm
+
+# Collect all .c files under lib/
+SRCS = $(shell find lib -name '*.c')
+OBJS = $(patsubst lib/%.c, build/%.o, $(SRCS))
+
+.PHONY: all clean test
+
+all: build/liblzgraph.a
+
+# Static library
+build/liblzgraph.a: $(OBJS)
+	ar rcs $@ $^
+
+# Compile each .c → .o, mirroring the lib/ directory structure in build/
+build/%.o: lib/%.c | build_dirs
+	$(CC) $(CFLAGS) -c $< -o $@
+
+# Create build subdirectories matching lib/
+build_dirs:
+	@mkdir -p $(sort $(dir $(OBJS)))
+
+# Test runners
+test: test_core test_graph test_forward test_simulate test_analytics test_occupancy test_io_posterior test_pgen_dist test_variants test_gene_data test_sharing test_graph_ops test_diversity test_features test_genomic_simulate test_walk_dict
+
+test_core: build/test_core
+	./build/test_core
+
+test_graph: build/test_graph
+	./build/test_graph
+
+build/test_core: tests/c_unit/test_core.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+build/test_graph: tests/c_unit/test_graph.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_forward: build/test_forward
+	./build/test_forward
+
+build/test_forward: tests/c_unit/test_forward.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_simulate: build/test_simulate
+	./build/test_simulate
+
+build/test_simulate: tests/c_unit/test_simulate.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_analytics: build/test_analytics
+	./build/test_analytics
+
+build/test_analytics: tests/c_unit/test_analytics.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_occupancy: build/test_occupancy
+	./build/test_occupancy
+
+build/test_occupancy: tests/c_unit/test_occupancy.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_io_posterior: build/test_io_posterior
+	./build/test_io_posterior
+
+build/test_io_posterior: tests/c_unit/test_io_posterior.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_pgen_dist: build/test_pgen_dist
+	./build/test_pgen_dist
+
+build/test_pgen_dist: tests/c_unit/test_pgen_dist.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_variants: build/test_variants
+	./build/test_variants
+
+build/test_variants: tests/c_unit/test_variants.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_gene_data: build/test_gene_data
+	./build/test_gene_data
+
+build/test_gene_data: tests/c_unit/test_gene_data.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_sharing: build/test_sharing
+	./build/test_sharing
+
+build/test_sharing: tests/c_unit/test_sharing.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_graph_ops: build/test_graph_ops
+	./build/test_graph_ops
+
+build/test_graph_ops: tests/c_unit/test_graph_ops.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_diversity: build/test_diversity
+	./build/test_diversity
+
+build/test_diversity: tests/c_unit/test_diversity.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_features: build/test_features
+	./build/test_features
+
+build/test_features: tests/c_unit/test_features.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_genomic_simulate: build/test_genomic_simulate
+	./build/test_genomic_simulate
+
+build/test_genomic_simulate: tests/c_unit/test_genomic_simulate.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+test_walk_dict: build/test_walk_dict
+	./build/test_walk_dict
+
+build/test_walk_dict: tests/c_unit/test_walk_dict.c build/liblzgraph.a | build_dirs
+	$(CC) $(CFLAGS) $< -Lbuild -llzgraph $(LDFLAGS) -o $@
+
+clean:
+	rm -rf build

lzgraphs-3.0.1/PKG-INFO

@@ -0,0 +1,246 @@
+Metadata-Version: 2.4
+Name: LZGraphs
+Version: 3.0.1
+Summary: High-performance LZ76 compression graphs for immune receptor repertoire analysis
+Author-email: Thomas Konstantinovsky <thomaskon90@gmail.com>
+Maintainer-email: Thomas Konstantinovsky <thomaskon90@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/MuteJester/LZGraphs
+Project-URL: Documentation, https://mutejester.github.io/LZGraphs/
+Project-URL: Repository, https://github.com/MuteJester/LZGraphs
+Project-URL: Issues, https://github.com/MuteJester/LZGraphs/issues
+Project-URL: Changelog, https://github.com/MuteJester/LZGraphs/blob/master/CHANGELOG.md
+Keywords: Graph Theory,Immunology,Analytics,Biology,T-cell,Repertoire,CDR3,Bioinformatics,LZ76,Lempel-Ziv
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: C
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == "viz"
+Requires-Dist: seaborn>=0.12; extra == "viz"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: scipy>=1.9; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
+Dynamic: license-file
+
+<p align="center">
+  <a href="https://github.com/MuteJester/LZGraphs">
+    <img src="docs/images/lzglogo2.png" alt="LZGraphs" width="400">
+  </a>
+</p>
+
+<p align="center">
+  <strong>High-performance LZ76 compression graphs for immune receptor repertoire analysis</strong>
+</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/v/LZGraphs.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/pyversions/LZGraphs.svg" alt="Python"></a>
+  <a href="https://github.com/MuteJester/LZGraphs/blob/master/LICENSE"><img src="https://img.shields.io/github/license/MuteJester/LZGraphs.svg" alt="License"></a>
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/dm/LZGraphs.svg" alt="Downloads"></a>
+  <a href="https://github.com/MuteJester/LZGraphs/stargazers"><img src="https://img.shields.io/github/stars/MuteJester/LZGraphs.svg" alt="Stars"></a>
+</p>
+
+<p align="center">
+  <a href="https://MuteJester.github.io/LZGraphs/"><strong>Documentation</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://MuteJester.github.io/LZGraphs/getting-started/quickstart/"><strong>Quick Start</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://MuteJester.github.io/LZGraphs/api/lzgraph/"><strong>API Reference</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://github.com/MuteJester/LZGraphs/issues">Report Bug</a>
+</p>
+
+---
+
+**LZGraphs** is a Python library that transforms T-cell and B-cell receptor CDR3 sequences into probabilistic directed graphs using the Lempel-Ziv 76 compression algorithm. Built on a C core with Python bindings, it provides:
+
+- **Exact generation probabilities** for any CDR3 sequence
+- **LZ76-constrained sequence simulation** that guarantees valid outputs
+- **Analytical diversity metrics** (Hill numbers, richness predictions, sharing spectra)
+- **Graph algebra** (union, intersection, difference) for repertoire comparison
+- **ML feature extraction** with fixed-size vectors for classification pipelines
+- **Bayesian posterior personalization** to adapt population models to individuals
+- **A CLI tool** (`lzg`) for terminal-based analysis
+
+## Quick Start
+
+```bash
+pip install LZGraphs
+```
+
+```python
+from LZGraphs import LZGraph
+
+# Build a graph from CDR3 amino acid sequences
+graph = LZGraph(
+    ['CASSLEPSGGTDTQYF', 'CASSDTSGGTDTQYF', 'CASSLEPQTFTDTFFF',
+     'CASSLGQGSTEAFF', 'CASSLGIRRT'],
+    variant='aap',
+)
+
+# Score a sequence
+log_p = graph.lzpgen('CASSLEPSGGTDTQYF')
+print(f"log P(gen) = {log_p:.2f}")
+
+# Simulate new sequences
+result = graph.simulate(1000, seed=42)
+print(f"Generated {len(result)} sequences")
+
+# Diversity
+print(f"D(1) = {graph.effective_diversity():.1f}")
+print(f"D(2) = {graph.hill_number(2):.1f}")
+```
+
+### With gene annotation
+
+```python
+graph = LZGraph(
+    sequences,
+    variant='aap',
+    v_genes=['TRBV16-1*01', 'TRBV1-1*01', ...],
+    j_genes=['TRBJ1-2*01', 'TRBJ1-5*01', ...],
+)
+
+# Gene-constrained simulation
+result = graph.simulate(100, sample_genes=True, seed=42)
+print(result.v_genes[0], result.j_genes[0])
+```
+
+### Command line
+
+```bash
+lzg build repertoire.tsv -o rep.lzg
+lzg score rep.lzg sequences.txt
+lzg diversity rep.lzg
+lzg simulate rep.lzg -n 10000 --seed 42
+lzg compare healthy.lzg disease.lzg
+```
+
+## Graph Variants
+
+One unified `LZGraph` class with three encoding schemes:
+
+| Variant | Input | Node format | Best for |
+|---------|-------|-------------|----------|
+| `'aap'` | Amino acid CDR3 | `C_2`, `SL_6` | Most TCR/BCR analysis |
+| `'ndp'` | Nucleotide CDR3 | `TG0_4` | Nucleotide-level analysis |
+| `'naive'` | Any strings | `C`, `SL` | Motif discovery, ML features |
+
+## Key Capabilities
+
+### Scoring & Simulation
+
+```python
+# Log-probability of a sequence
+graph.lzpgen('CASSLEPSGGTDTQYF')              # single
+graph.lzpgen(['seq1', 'seq2', 'seq3'])         # batch → np.ndarray
+
+# Simulate with optional gene constraints
+result = graph.simulate(1000, seed=42)
+result = graph.simulate(100, v_gene='TRBV5-1*01', j_gene='TRBJ2-7*01')
+```
+
+### Diversity & Analytics
+
+```python
+graph.effective_diversity()          # exp(Shannon entropy)
+graph.hill_number(2)                 # inverse Simpson
+graph.hill_numbers([0, 1, 2, 5])     # multiple orders → np.ndarray
+graph.predicted_richness(100_000)    # expected unique seqs at depth
+graph.predicted_overlap(10000, 50000)# expected shared sequences
+graph.pgen_distribution()            # analytical Gaussian mixture
+```
+
+### Graph Algebra
+
+```python
+combined = graph_a | graph_b          # union
+shared   = graph_a & graph_b          # intersection
+unique_a = graph_a - graph_b          # difference
+personal = population.posterior(patient_seqs, kappa=10.0)  # Bayesian update
+```
+
+### Repertoire Comparison
+
+```python
+from LZGraphs import jensen_shannon_divergence
+jsd = jensen_shannon_divergence(graph_a, graph_b)  # 0 = identical, 1 = max different
+```
+
+### ML Feature Extraction
+
+```python
+# Project any repertoire into a fixed reference space
+features = reference.feature_aligned(LZGraph(sample_seqs, variant='aap'))
+stats = graph.feature_stats()           # 15-element summary vector
+profile = graph.feature_mass_profile()  # position-based mass distribution
+```
+
+### Serialization
+
+```python
+graph.save('repertoire.lzg')           # fast binary format
+loaded = LZGraph.load('repertoire.lzg')
+```
+
+## Documentation
+
+Full documentation with tutorials, concept guides, and API reference:
+
+**[https://MuteJester.github.io/LZGraphs/](https://MuteJester.github.io/LZGraphs/)**
+
+- [Quick Start](https://MuteJester.github.io/LZGraphs/getting-started/quickstart/) — build your first graph in 5 minutes
+- [Tutorials](https://MuteJester.github.io/LZGraphs/tutorials/) — graph construction, sequence analysis, diversity metrics
+- [API Reference](https://MuteJester.github.io/LZGraphs/api/lzgraph/) — complete class and function reference
+- [CLI Reference](https://MuteJester.github.io/LZGraphs/api/cli/) — terminal tool documentation
+
+## Citation
+
+If you use LZGraphs in your research, please cite:
+
+```bibtex
+@article{konstantinovsky2023lzgraphs,
+  title={A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding
+         Using Lossless String Compression},
+  author={Konstantinovsky, Thomas and Nagar, Maor and Louzoun, Yoram},
+  journal={Bioinformatics},
+  year={2023},
+  publisher={Oxford University Press}
+}
+```
+
+## Contributing
+
+Contributions are welcome. Please open an issue or submit a pull request.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/my-feature`)
+3. Commit your changes
+4. Push and open a Pull Request
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.
+
+## Contact
+
+Thomas Konstantinovsky — [thomaskon90@gmail.com](mailto:thomaskon90@gmail.com)
+
+[GitHub](https://github.com/MuteJester/LZGraphs) · [PyPI](https://pypi.org/project/LZGraphs/) · [Documentation](https://MuteJester.github.io/LZGraphs/)

lzgraphs-3.0.1/README.md

@@ -0,0 +1,202 @@
+<p align="center">
+  <a href="https://github.com/MuteJester/LZGraphs">
+    <img src="docs/images/lzglogo2.png" alt="LZGraphs" width="400">
+  </a>
+</p>
+
+<p align="center">
+  <strong>High-performance LZ76 compression graphs for immune receptor repertoire analysis</strong>
+</p>
+
+<p align="center">
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/v/LZGraphs.svg" alt="PyPI"></a>
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/pyversions/LZGraphs.svg" alt="Python"></a>
+  <a href="https://github.com/MuteJester/LZGraphs/blob/master/LICENSE"><img src="https://img.shields.io/github/license/MuteJester/LZGraphs.svg" alt="License"></a>
+  <a href="https://pypi.org/project/LZGraphs/"><img src="https://img.shields.io/pypi/dm/LZGraphs.svg" alt="Downloads"></a>
+  <a href="https://github.com/MuteJester/LZGraphs/stargazers"><img src="https://img.shields.io/github/stars/MuteJester/LZGraphs.svg" alt="Stars"></a>
+</p>
+
+<p align="center">
+  <a href="https://MuteJester.github.io/LZGraphs/"><strong>Documentation</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://MuteJester.github.io/LZGraphs/getting-started/quickstart/"><strong>Quick Start</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://MuteJester.github.io/LZGraphs/api/lzgraph/"><strong>API Reference</strong></a> &nbsp;&middot;&nbsp;
+  <a href="https://github.com/MuteJester/LZGraphs/issues">Report Bug</a>
+</p>
+
+---
+
+**LZGraphs** is a Python library that transforms T-cell and B-cell receptor CDR3 sequences into probabilistic directed graphs using the Lempel-Ziv 76 compression algorithm. Built on a C core with Python bindings, it provides:
+
+- **Exact generation probabilities** for any CDR3 sequence
+- **LZ76-constrained sequence simulation** that guarantees valid outputs
+- **Analytical diversity metrics** (Hill numbers, richness predictions, sharing spectra)
+- **Graph algebra** (union, intersection, difference) for repertoire comparison
+- **ML feature extraction** with fixed-size vectors for classification pipelines
+- **Bayesian posterior personalization** to adapt population models to individuals
+- **A CLI tool** (`lzg`) for terminal-based analysis
+
+## Quick Start
+
+```bash
+pip install LZGraphs
+```
+
+```python
+from LZGraphs import LZGraph
+
+# Build a graph from CDR3 amino acid sequences
+graph = LZGraph(
+    ['CASSLEPSGGTDTQYF', 'CASSDTSGGTDTQYF', 'CASSLEPQTFTDTFFF',
+     'CASSLGQGSTEAFF', 'CASSLGIRRT'],
+    variant='aap',
+)
+
+# Score a sequence
+log_p = graph.lzpgen('CASSLEPSGGTDTQYF')
+print(f"log P(gen) = {log_p:.2f}")
+
+# Simulate new sequences
+result = graph.simulate(1000, seed=42)
+print(f"Generated {len(result)} sequences")
+
+# Diversity
+print(f"D(1) = {graph.effective_diversity():.1f}")
+print(f"D(2) = {graph.hill_number(2):.1f}")
+```
+
+### With gene annotation
+
+```python
+graph = LZGraph(
+    sequences,
+    variant='aap',
+    v_genes=['TRBV16-1*01', 'TRBV1-1*01', ...],
+    j_genes=['TRBJ1-2*01', 'TRBJ1-5*01', ...],
+)
+
+# Gene-constrained simulation
+result = graph.simulate(100, sample_genes=True, seed=42)
+print(result.v_genes[0], result.j_genes[0])
+```
+
+### Command line
+
+```bash
+lzg build repertoire.tsv -o rep.lzg
+lzg score rep.lzg sequences.txt
+lzg diversity rep.lzg
+lzg simulate rep.lzg -n 10000 --seed 42
+lzg compare healthy.lzg disease.lzg
+```
+
+## Graph Variants
+
+One unified `LZGraph` class with three encoding schemes:
+
+| Variant | Input | Node format | Best for |
+|---------|-------|-------------|----------|
+| `'aap'` | Amino acid CDR3 | `C_2`, `SL_6` | Most TCR/BCR analysis |
+| `'ndp'` | Nucleotide CDR3 | `TG0_4` | Nucleotide-level analysis |
+| `'naive'` | Any strings | `C`, `SL` | Motif discovery, ML features |
+
+## Key Capabilities
+
+### Scoring & Simulation
+
+```python
+# Log-probability of a sequence
+graph.lzpgen('CASSLEPSGGTDTQYF')              # single
+graph.lzpgen(['seq1', 'seq2', 'seq3'])         # batch → np.ndarray
+
+# Simulate with optional gene constraints
+result = graph.simulate(1000, seed=42)
+result = graph.simulate(100, v_gene='TRBV5-1*01', j_gene='TRBJ2-7*01')
+```
+
+### Diversity & Analytics
+
+```python
+graph.effective_diversity()          # exp(Shannon entropy)
+graph.hill_number(2)                 # inverse Simpson
+graph.hill_numbers([0, 1, 2, 5])     # multiple orders → np.ndarray
+graph.predicted_richness(100_000)    # expected unique seqs at depth
+graph.predicted_overlap(10000, 50000)# expected shared sequences
+graph.pgen_distribution()            # analytical Gaussian mixture
+```
+
+### Graph Algebra
+
+```python
+combined = graph_a | graph_b          # union
+shared   = graph_a & graph_b          # intersection
+unique_a = graph_a - graph_b          # difference
+personal = population.posterior(patient_seqs, kappa=10.0)  # Bayesian update
+```
+
+### Repertoire Comparison
+
+```python
+from LZGraphs import jensen_shannon_divergence
+jsd = jensen_shannon_divergence(graph_a, graph_b)  # 0 = identical, 1 = max different
+```
+
+### ML Feature Extraction
+
+```python
+# Project any repertoire into a fixed reference space
+features = reference.feature_aligned(LZGraph(sample_seqs, variant='aap'))
+stats = graph.feature_stats()           # 15-element summary vector
+profile = graph.feature_mass_profile()  # position-based mass distribution
+```
+
+### Serialization
+
+```python
+graph.save('repertoire.lzg')           # fast binary format
+loaded = LZGraph.load('repertoire.lzg')
+```
+
+## Documentation
+
+Full documentation with tutorials, concept guides, and API reference:
+
+**[https://MuteJester.github.io/LZGraphs/](https://MuteJester.github.io/LZGraphs/)**
+
+- [Quick Start](https://MuteJester.github.io/LZGraphs/getting-started/quickstart/) — build your first graph in 5 minutes
+- [Tutorials](https://MuteJester.github.io/LZGraphs/tutorials/) — graph construction, sequence analysis, diversity metrics
+- [API Reference](https://MuteJester.github.io/LZGraphs/api/lzgraph/) — complete class and function reference
+- [CLI Reference](https://MuteJester.github.io/LZGraphs/api/cli/) — terminal tool documentation
+
+## Citation
+
+If you use LZGraphs in your research, please cite:
+
+```bibtex
+@article{konstantinovsky2023lzgraphs,
+  title={A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding
+         Using Lossless String Compression},
+  author={Konstantinovsky, Thomas and Nagar, Maor and Louzoun, Yoram},
+  journal={Bioinformatics},
+  year={2023},
+  publisher={Oxford University Press}
+}
+```
+
+## Contributing
+
+Contributions are welcome. Please open an issue or submit a pull request.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/my-feature`)
+3. Commit your changes
+4. Push and open a Pull Request
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.
+
+## Contact
+
+Thomas Konstantinovsky — [thomaskon90@gmail.com](mailto:thomaskon90@gmail.com)
+
+[GitHub](https://github.com/MuteJester/LZGraphs) · [PyPI](https://pypi.org/project/LZGraphs/) · [Documentation](https://MuteJester.github.io/LZGraphs/)