https://lessup.github.io/awesome-bioinfo-algorithms/

Curated bioinformatics algorithms knowledge base with complexity analysis, CLI maintenance tools, and bilingual docs.
https://lessup.github.io/awesome-bioinfo-algorithms/
algorithms awesome-list bioinformatics computational-biology genomics graph-genomics metagenomics phylogenetics protein-language-model protein-structure sequence-alignment single-cell variant-calling
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Curated bioinformatics algorithms knowledge base with complexity analysis, CLI maintenance tools, and bilingual docs.
Host: GitHub
URL: https://lessup.github.io/awesome-bioinfo-algorithms/
Owner: LessUp
License: cc0-1.0
Created: 2026-01-03T07:16:14.000Z (5 months ago)
Default Branch: master
Last Pushed: 2026-05-12T09:22:42.000Z (17 days ago)
Last Synced: 2026-05-12T11:25:35.217Z (17 days ago)
Topics: algorithms, awesome-list, bioinformatics, computational-biology, genomics, graph-genomics, metagenomics, phylogenetics, protein-language-model, protein-structure, sequence-alignment, single-cell, variant-calling
Language: Python
Homepage: https://lessup.github.io/awesome-bioinfo-algorithms/
Size: 937 KB
Stars: 3
Watchers: 0
Forks: 0
Open Issues: 5
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Codeowners: .github/CODEOWNERS
- Security: SECURITY.md
- Agents: AGENTS.md
Awesome Lists containing this project

README

          
Awesome Bioinformatics Algorithms




  

  

  

  

  





  

  

  

  





  🧬 A curated collection of bioinformatics algorithms with complexity analysis





  简体中文 • 

  📖 Documentation Site • 

  🤝 Contributing • 

  📚 Citation



---

## ✨ Highlights

**🎯 For Researchers**

- 195+ curated algorithms

- Time/space complexity analysis

- Paper and implementation links

- Multi-language support

**💻 For Developers**

- CLI toolkit for data management

- Automated validation & generation

- Structured YAML data format

- Extensive test coverage

---

## 🚀 Quick Start

```bash

# Clone repository

git clone https://github.com/LessUp/awesome-bioinfo-algorithms.git

cd awesome-bioinfo-algorithms

# Install dependencies (includes MkDocs support)

pip install -e ".[dev,docs]"

# Validate data

python -m awesome_bioinfo validate

# Show statistics

python -m awesome_bioinfo stats

```

---

## 📊 Statistics

| Metric | Value |

|:-------|------:|

| Total Algorithms | **195** |

| Categories | **16** |

| Unique Tags | **392** |

---

## 📑 Table of Contents

Click to expand

- [Sequence Alignment](#sequence-alignment)

- [Sequence Assembly](#sequence-assembly)

- [Variant Calling](#variant-calling)

- [Gene Expression Analysis](#gene-expression-analysis)

- [Protein Structure Prediction](#protein-structure-prediction)

- [Phylogenetics](#phylogenetics)

- [Functional Annotation](#functional-annotation)

- [Data Compression](#data-compression)

- [Single-Cell Genomics](#single-cell-genomics)

- [Metagenomics](#metagenomics)

- [Epigenomics](#epigenomics)

- [Gene Prediction](#gene-prediction)

- [Population Genetics](#population-genetics)

- [Spatial Omics](#spatial-omics)

- [Graph Genomics](#graph-genomics)

- [Protein Language Model](#protein-language-model)

---

## Category Overview

| Category | Algorithms | Description |

|----------|------------|-------------|

| Sequence Alignment | 19 | Algorithms for comparing and aligning biological sequences |

| Sequence Assembly | 14 | Algorithms for reconstructing complete sequences from short reads |

| Variant Calling | 14 | Algorithms for detecting genomic variations |

| Gene Expression Analysis | 12 | Algorithms for analyzing gene expression levels |

| Protein Structure Prediction | 14 | Algorithms for predicting protein 3D structures |

| Phylogenetics | 12 | Algorithms for building and analyzing evolutionary trees |

| Functional Annotation | 12 | Algorithms for predicting gene and protein functions |

| Data Compression | 10 | Algorithms for compressing bioinformatics data |

| Single-Cell Genomics | 15 | Algorithms for single-cell genomics and transcriptomics |

| Metagenomics | 14 | Algorithms for microbial community genomics |

| Epigenomics | 6 | Algorithms for analyzing epigenetic modifications |

| Gene Prediction | 12 | Algorithms for gene structure prediction and annotation |

| Population Genetics | 12 | Algorithms for population genetic structure and evolution |

| Spatial Omics | 10 | Algorithms for spatially-resolved omics data |

| Graph Genomics | 9 | Algorithms based on graph representations of genomes |

| Protein Language Model | 10 | Protein analysis using large-scale pre-trained models |

---

## Featured Algorithms

### Sequence Alignment 

↑ Back to Top

**Pairwise Alignment**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| ⭐ BLAST | 1990 | O(mn) | O(mn) | `heuristic` `database-search` `classic` |

| ⭐ Smith-Waterman | 1981 | O(mn) | O(mn) | `dynamic-programming` `local-alignment` `classic` |

| ⭐ Needleman-Wunsch | 1970 | O(mn) | O(mn) | `dynamic-programming` `global-alignment` `classic` |

| 🆕 WFA2-lib | 2023 | O(ns) | O(s) | `wavefront` `adaptive` `ultra-fast` |

| Minimap2 | 2018 | O(n) | O(n) | `minimizer` `long-read` `versatile` |

*[View all 14 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Multiple Sequence Alignment**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Clustal Omega | 2011 | O(n * L^2) | O(n * L) | `multiple-alignment` `guide-tree` `progressive` |

| Kalign | 2005 | O(n^2 * L) | O(n * L) | `multiple-alignment` `fast` `wu-manber` |

| MUSCLE | 2004 | O(n^2 * L) | O(n * L) | `multiple-alignment` `iterative` `refinement` |

| MAFFT | 2002 | O(n * L * log L) | O(n * L) | `fft` `multiple-alignment` `scalable` |

| POA | 2002 | O(n^2 * L^2) | O(n * L^2) | `multiple-alignment` `partial-order` `graph-based` |

### Sequence Assembly 

↑ Back to Top

**De Novo Assembly**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 Verkko | 2023 | O(n log n) | O(n) | `t2t` `hybrid` `hifi` |

| Hifiasm | 2021 | O(n log n) | O(n) | `hifi` `haplotype-aware` `long-read` |

| Shasta | 2020 | O(n) | O(n) | `long-read` `fast` `run-length` |

| Flye | 2019 | O(n log n) | O(n) | `repeat-graph` `long-read` `ont` |

| Wtdbg2 | 2019 | O(n) | O(n) | `long-read` `fuzzy-bruijn` `fast` |

*[View all 12 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Reference-Guided Assembly**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| RagTag | 2022 | O(n log n) | O(n) | `reference-based` `scaffolding` `assembly-polishing` |

| Reference-Guided Assembly | 2011 | O(n log n) | O(n) | `reference-based` `scaffolding` `resequencing` |

### Variant Calling 

↑ Back to Top

**SNV Detection**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 DeepSomatic | 2024 | O(n * r) | O(r) | `deep-learning` `somatic` `cancer` |

| Clair3 | 2022 | O(n * r) | O(r) | `long-read` `nanopore` `pacbio` |

| Octopus | 2021 | O(n * h) | O(h) | `bayesian` `haplotype` `germline-somatic` |

| DeepVariant | 2018 | O(n * r) | O(r) | `deep-learning` `cnn` `snp` |

| Strelka2 | 2018 | O(n * r) | O(r) | `somatic` `germline` `fast` |

*[View all 8 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Structural Variants**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 Sniffles2 | 2023 | O(n * c) | O(n) | `structural-variant` `long-read` `breakpoint` |

| cuteSV | 2020 | O(n * c) | O(n) | `structural-variant` `long-read` `clustering` |

| GRIDSS | 2017 | O(n * c) | O(n) | `structural-variant` `breakend` `assembly-based` |

| Manta | 2016 | O(n * c) | O(c) | `structural-variant` `graph-assembly` `clinical` |

| SvABA | 2016 | O(n * c) | O(c) | `structural-variant` `somatic` `assembly-based` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

### Gene Expression Analysis 

↑ Back to Top

**Expression Quantification**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Salmon | 2017 | O(n) | O(t) | `selective-alignment` `quantification` `rna-seq` |

| Kallisto | 2016 | O(n) | O(t) | `pseudoalignment` `quantification` `rna-seq` |

| tximport | 2016 | O(n * t) | O(g) | `import` `summarization` `offset-correction` |

| StringTie | 2015 | O(n) | O(g) | `transcript-assembly` `quantification` `rna-seq` |

| STAR | 2013 | O(n) | O(g) | `rna-seq` `splice-aware` `alignment` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Differential Expression**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Sleuth | 2017 | O(n * g) | O(g) | `differential-expression` `bootstrap` `rna-seq` |

| NOISeq | 2015 | O(n * g) | O(g) | `differential-expression` `non-parametric` `noiseq` |

| DESeq2 | 2014 | O(n * g) | O(g) | `rna-seq` `differential-expression` `negative-binomial` |

| limma-voom | 2014 | O(n * g) | O(g) | `differential-expression` `precision-weight` `linear-model` |

| Ballgown | 2014 | O(n * g) | O(g) | `differential-expression` `fpkm` `transcript-level` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

### Protein Structure Prediction 

↑ Back to Top

**Ab Initio Prediction**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 AlphaFold3 | 2024 | O(n^2) | O(n^2) | `deep-learning` `structure-prediction` `multi-modal` |

| 🆕 Chai-1 | 2024 | O(n^2) | O(n^2) | `structure-prediction` `multi-modal` `drug-discovery` |

| 🆕 Boltz-1 | 2024 | O(n^2) | O(n^2) | `structure-prediction` `open-source` `diffusion` |

| 🆕 ESMFold | 2023 | O(n^2) | O(n^2) | `language-model` `single-sequence` `fast` |

| OmegaFold | 2022 | O(n^2) | O(n^2) | `language-model` `single-sequence` `structure-prediction` |

*[View all 9 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Template-Based Modeling**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 Foldseek | 2023 | O(n) | O(n) | `structure-search` `fast` `3Di` |

| I-TASSER | 2008 | O(n^3) | O(n^2) | `threading` `template-based` `fragment-assembly` |

| TM-align | 2005 | O(n^3) | O(n^2) | `structure-alignment` `rmsd` `classic` |

| Rosetta | 2003 | O(n^3) | O(n^2) | `energy-function` `monte-carlo` `protein-design` |

| MODELLER | 1993 | O(n^2) | O(n^2) | `homology-modeling` `template-based` `comparative-modeling` |

### Phylogenetics 

↑ Back to Top

**Distance Methods**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| ⭐ Neighbor-Joining | 1987 | O(n^3) | O(n^2) | `distance-based` `tree-building` `classic` |

| FastTree | 2010 | O(n * s * log n) | O(n * s) | `tree-building` `approximate-likelihood` `scalable` |

**Character-Based Methods**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| IQ-TREE 2 | 2020 | O(n^2 * s) | O(n * s) | `maximum-likelihood` `model-finder` `partition` |

| RAxML-NG | 2019 | O(n^2 * s * r) | O(n * s) | `maximum-likelihood` `scalable` `ultrafast-bootstrap` |

| ASTRAL | 2018 | O(n * m) | O(n * m) | `species-tree` `summary-method` `coalescent` |

| RevBayes | 2016 | O(n^2 * s * r) | O(n * s) | `bayesian` `probabilistic-programming` `flexible` |

| IQ-TREE | 2015 | O(n^2 * s) | O(n * s) | `maximum-likelihood` `model-selection` `ultrafast-bootstrap` |

*[View all 10 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

### Functional Annotation 

↑ Back to Top

**Homology-Based**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| ⭐ BLAST-based Annotation | 1990 | O(mn) | O(m) | `sequence-similarity` `database-search` `classic` |

| Bakta | 2021 | O(n) | O(n) | `prokaryotic` `annotation` `standardized` |

| KofamKOALA | 2020 | O(n * m) | O(m) | `kegg` `orthology` `annotation` |

| OrthoFinder | 2019 | O(n^2) | O(n^2) | `orthology` `comparative-genomics` `gene-family` |

| eggNOG-mapper | 2017 | O(n * m) | O(m) | `orthology` `go-annotation` `kegg` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Domain-Based**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| SignalP | 2019 | O(n) | O(n) | `signal-peptide` `deep-learning` `secretion` |

| InterProScan | 2014 | O(m * d) | O(m) | `multi-database` `domain-detection` `go-annotation` |

| InterPro | 2014 | O(m * d) | O(m) | `database` `domain` `protein-family` |

| HMMER | 2011 | O(mn) | O(m) | `hmm` `domain-detection` `remote-homology` |

| PfamScan | 2011 | O(mn) | O(m) | `domain-detection` `pfam` `protein-family` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

### Data Compression 

↑ Back to Top

**Specialized Compression**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Genozip | 2021 | O(n) | O(1) | `multi-format` `high-ratio` `random-access` |

| SPRING Compress | 2020 | O(n log n) | O(n) | `fastq` `reordering` `high-ratio` |

| SPRING | 2019 | O(n) | O(n) | `fastq` `specialized-compression` `high-ratio` |

| MANGO | 2018 | O(n) | O(n) | `reference-free` `genome-compression` `context-modeling` |

| Orione | 2015 | O(n) | O(1) | `reference-assisted` `fastq` `sam` |

*[View all 8 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**General Compression**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| BGZF and Tabix | 2011 | O(n) | O(1) | `block-compression` `indexing` `random-access` |

| GZIP for FASTQ | 1992 | O(n) | O(1) | `lossless` `general-purpose` `standard` |

### Single-Cell Genomics 

↑ Back to Top

**Cell Clustering & Annotation**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 scVI-tools | 2023 | O(c * g * e) | O(c * g) | `variational-autoencoder` `deep-learning` `batch-correction` |

| scArches | 2022 | O(c * g * e) | O(c * g) | `reference-mapping` `transfer-learning` `surgery` |

| CellTypist | 2022 | O(c * g) | O(c * g) | `cell-type` `annotation` `logistic-regression` |

| scANVI | 2021 | O(c * g * e) | O(c * g) | `semi-supervised` `annotation` `deep-learning` |

| SCENIC | 2020 | O(c * g^2) | O(c * g) | `regulatory-network` `transcription-factor` `grn` |

*[View all 10 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Preprocessing**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| alevin-fry | 2022 | O(n * k) | O(g) | `quantification` `memory-efficient` `simpleaf` |

| STARsolo | 2021 | O(n * g) | O(c * g) | `preprocessing` `alignment` `umi` |

| kallisto | bustools | 2021 | O(n * k) | O(g) | `preprocessing` `pseudoalignment` `fast` |

| Alevin | 2019 | O(n * g) | O(c * g) | `preprocessing` `umi` `lightweight-mapping` |

| Cell Ranger | 2017 | O(n * g) | O(c * g) | `10x-genomics` `preprocessing` `umi` |

### Metagenomics 

↑ Back to Top

**Taxonomic Profiling**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 MetaPhlAn 4 | 2023 | O(n * m) | O(m) | `marker-gene` `profiling` `enhanced` |

| Kraken2 | 2019 | O(n * k) | O(d) | `k-mer` `classification` `fast` |

| QIIME 2 | 2019 | O(n * d) | O(n) | `pipeline` `microbiome` `diversity` |

| MetaBAT 2 | 2019 | O(n * c) | O(n) | `binning` `metagenome` `adaptive` |

| mOTUs | 2017 | O(n * m) | O(m) | `marker-gene` `profiling` `universal` |

*[View all 9 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Functional Profiling**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| metaPOST | 2021 | O(n * c) | O(n) | `post-processing` `refinement` `assembly` |

| MetaBAT 2 | 2019 | O(n * c) | O(n) | `binning` `mags` `coverage` |

| HUMAnN 3 | 2018 | O(n * d) | O(d) | `functional-profiling` `pathway` `gene-families` |

| MaxBin 2 | 2016 | O(n * c) | O(n) | `binning` `expectation-maximization` `mags` |

| HUMAnN | 2014 | O(n * d) | O(d) | `pathway-analysis` `gene-family` `functional` |

### Epigenomics 

↑ Back to Top

**ChIP-seq Analysis**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| HMMRATAC | 2019 | O(n) | O(n) | `atac-seq` `hmm` `peak-calling` |

| ChromHMM | 2012 | O(n * s^2) | O(n * s) | `hmm` `chromatin-state` `histone` |

| MACS2 | 2008 | O(n) | O(n) | `peak-calling` `chip-seq` `histone` |

**Methylation Analysis**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| DSS | 2014 | O(n * s) | O(n) | `methylation` `beta-binomial` `dmr` |

| methylKit | 2012 | O(n * s) | O(n) | `methylation` `differential-analysis` `rrbs` |

| Bismark | 2011 | O(n * g) | O(g) | `bisulfite-seq` `methylation` `cpg` |

### Gene Prediction 

↑ Back to Top

**Eukaryotic Gene Prediction**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| BRAKER | 2016 | O(n * g) | O(n) | `pipeline` `evidence-based` `automated` |

| MAKER | 2008 | O(n * g) | O(n) | `annotation-pipeline` `evidence-based` `eukaryotic` |

| AUGUSTUS | 2005 | O(n * s^2) | O(n * s) | `gene-prediction` `eukaryotic` `hmm` |

| SNAP | 2004 | O(n * s) | O(n) | `semi-hmm` `ab-initio` `eukaryotic` |

| AUGUSTUS | 2003 | O(n * s^2) | O(n * s) | `ghmm` `ab-initio` `exon-intron` |

**Prokaryotic Gene Prediction**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Prodigal | 2010 | O(n) | O(n) | `prokaryotic` `self-training` `metagenome` |

| Prodigal | 2010 | O(n) | O(n) | `gene-prediction` `prokaryotic` `fast` |

| RNAmmer | 2007 | O(n * s) | O(n) | `rrna` `gene-prediction` `hmm` |

| GeneMark-ES | 2005 | O(n) | O(n) | `gene-prediction` `hmm` `prokaryotic` |

| GLIMMER | 1998 | O(n) | O(n) | `interpolated-markov-model` `prokaryotic` `gene-finding` |

*[View all 7 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

### Population Genetics 

↑ Back to Top

**Selection Signature Detection**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| ⭐ Tajima's D | 1989 | O(n * L) | O(L) | `neutrality-test` `selection` `classic` |

| PCAdapt | 2016 | O(n * m * k) | O(n * m) | `selection` `pca` `outlier-detection` |

| Selscan | 2014 | O(n * m) | O(n * m) | `selection` `haplotype` `ihs` |

| HapFLK | 2013 | O(n * m * K) | O(m * K) | `selection` `haplotype` `population-differentiation` |

| BayeScan | 2008 | O(m * k * n) | O(m * k) | `selection` `bayesian` `fst` |

**Genome-Wide Association Study**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| REGENIE | 2021 | O(n * m) | O(n * m) | `gwas` `scalable` `two-stage` |

| SAIGE | 2018 | O(n * m) | O(n * m) | `gwas` `mixed-model` `rare-variant` |

| BOLT-LMM | 2015 | O(n * m) | O(n * m) | `lmm` `gwas` `scalable` |

| PLINK | 2007 | O(n * m) | O(n * m) | `gwas` `association` `qc` |

**PCA & Population Structure**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| ADMIXTURE | 2009 | O(n * m * k) | O(n * m) | `ancestry` `maximum-likelihood` `population-structure` |

| PCA for Population Structure | 2006 | O(n * m * k) | O(n * m) | `pca` `population-structure` `ancestry` |

| STRUCTURE | 2000 | O(n * m * k * g) | O(n * k) | `bayesian` `mcmc` `population-structure` |

### Spatial Omics 

↑ Back to Top

**Spatial Transcriptomics**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Seurat Spatial | 2021 | O(c * g) | O(c * g) | `spatial` `clustering` `integration` |

| Giotto Suite | 2021 | O(c * g) | O(c * g) | `spatial` `multi-platform` `comprehensive` |

| Squidpy | 2021 | O(c * g) | O(c * g) | `spatial` `graph-analysis` `cell-interaction` |

| SPARK-X | 2021 | O(g * n) | O(n) | `spatial` `fast` `non-parametric` |

| stLearn | 2021 | O(c * g) | O(c * g) | `spatial` `image-integration` `trajectory` |

*[View all 7 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Spatial Proteomics**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| CellChat | 2021 | O(c^2 * g) | O(c^2) | `cell-communication` `ligand-receptor` `signaling` |

| Cellpose | 2020 | O(p) | O(p) | `segmentation` `deep-learning` `cell-detection` |

| StarDist | 2018 | O(p) | O(p) | `segmentation` `deep-learning` `cell-nuclei` |

### Graph Genomics 

↑ Back to Top

**Variation Graph**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 PanVC | 2023 | O(n * m) | O(n) | `pangenome` `variant-calling` `genotyping` |

| HiFiBD | 2022 | O(n * d) | O(n) | `variation-graph` `hifi` `genotyping` |

| GraphAligner | 2019 | O(n * d) | O(n) | `graph-alignment` `long-read` `variation-graph` |

| VG (Variation Graph) | 2017 | O(n log n) | O(n) | `variation-graph` `alignment` `variant-calling` |

| GCSA2 | 2017 | O(n) | O(n) | `indexing` `k-mer` `compressed-suffix-array` |

**Pangenome**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| Minigraph | 2020 | O(n log n) | O(n) | `pangenome` `graph-alignment` `minimizer` |

| odgi | 2020 | O(n) | O(n) | `pangenome` `graph-operations` `visualization` |

| seqwish | 2020 | O(n^2) | O(n^2) | `pangenome` `graph-construction` `alignment-to-graph` |

| Cactus | 2011 | O(n^2 * k) | O(n * k) | `pangenome` `alignment` `progressive` |

### Protein Language Model 

↑ Back to Top

**Protein Function Prediction**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 ESMFold | 2023 | O(n^2) | O(n^2) | `structure-prediction` `single-sequence` `fast` |

| 🆕 RFdiffusion | 2023 | O(n^2 * T) | O(n^2) | `diffusion-model` `protein-design` `structure-generation` |

| ProteinMPNN | 2022 | O(n^2 * d) | O(n^2) | `protein-design` `inverse-folding` `graph-neural-network` |

| ESM-1v | 2021 | O(n^2 * d) | O(n^2) | `variant-effect` `zero-shot` `pathogenicity` |

| ProGen | 2020 | O(n^2 * d) | O(n^2) | `generative` `protein-design` `conditional-generation` |

*[View all 6 algorithms in this category →](https://lessup.github.io/awesome-bioinfo-algorithms/)*

**Protein Language Model Pretraining**

| Algorithm | Year | Time | Space | Tags |

|-----------|------|------|-------|------|

| 🆕 Ankh | 2023 | O(n^2 * d) | O(n^2) | `language-model` `lightweight` `efficient` |

| ESM-2 | 2022 | O(n^2 * d) | O(n^2) | `language-model` `transformer` `representation-learning` |

| ProtTrans | 2021 | O(n^2 * d) | O(n^2) | `language-model` `transfer-learning` `representation-learning` |

| ProtBERT | 2020 | O(n^2 * d) | O(n^2) | `language-model` `bert` `sequence-embedding` |

---

## 🛠️ CLI Commands

```bash

# Search for algorithms

python -m awesome_bioinfo search "alignment"

# Get algorithm details

python -m awesome_bioinfo info smith-waterman

# Compare two algorithms

python -m awesome_bioinfo compare smith-waterman needleman-wunsch

# Export data to JSON

python -m awesome_bioinfo export --format json > algorithms.json

# Generate MkDocs site

python -m awesome_bioinfo mkdocs

# Generate README

python -m awesome_bioinfo generate

```

---

## 📚 Resources

### Learning Platforms

- [Rosalind](http://rosalind.info/) — Bioinformatics algorithm learning

- [NCBI](https://www.ncbi.nlm.nih.gov/) — National Center for Biotechnology

- [EBI](https://www.ebi.ac.uk/) — European Bioinformatics Institute

### Tools & Communities

- [Bioconductor](https://www.bioconductor.org/) — R bioinformatics toolkit

- [Galaxy](https://usegalaxy.org/) — Open analysis platform

- [BioStars](https://www.biostars.org/) — Bioinformatics Q&A

- [scverse](https://scverse.org/) — Single-cell Python ecosystem

---

## 🤝 Contributing

We welcome contributions! Please see our [Contributing Guide](CONTRIBUTING.md) for details.

### Contribution Types

- 🆕 **Add new algorithms**

- 📝 **Improve descriptions**

- 🔗 **Add references**

- 🐛 **Report and fix bugs**

- 📚 **Improve documentation**

---

## 📚 Citation

If you use this project in your research, please cite it as:

```bibtex

@software{awesome_bioinfo_algorithms,

  title = {Awesome Bioinformatics Algorithms},

  author = {{LessUp Community}},

  year = {2025},

  url = {https://github.com/LessUp/awesome-bioinfo-algorithms}

}

```

Or see [CITATION.cff](CITATION.cff) for more citation formats.

---

## 📄 License



  

    

  



This project is licensed under [CC0 1.0 Universal](https://creativecommons.org/publicdomain/zero/1.0/) (Public Domain).

You are free to:

- ✅ Copy, modify, distribute

- ✅ Use for commercial purposes

- ✅ No attribution required

---



  Made with ❤️ by the community


  © 2025-2026 LessUp Community
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