A pipeline to generate a phylogenetic tree from huge SNP data
☆94Dec 30, 2023Updated 2 years ago
Alternatives and similar repositories for SNPhylo
Users that are interested in SNPhylo are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis☆333Jul 7, 2023Updated 2 years ago
- R Package to Estimate Variable Recombination Rates using Population Genetic Data☆44Nov 13, 2019Updated 6 years ago
- ☆44May 8, 2024Updated last year
- PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files☆205Aug 15, 2024Updated last year
- R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)☆112Updated this week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A Python API and a command-line tool for the Tree of Life☆17Aug 28, 2020Updated 5 years ago
- ☆31Nov 25, 2019Updated 6 years ago
- LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files☆207Jul 5, 2025Updated 9 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆213Jan 17, 2024Updated 2 years ago
- Efficient Local Ancestry Inference☆17Nov 10, 2025Updated 5 months ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆186Dec 19, 2024Updated last year
- MODAS: Multi-Omics Data Association Study toolkit☆21Nov 21, 2024Updated last year
- ☆51Aug 27, 2019Updated 6 years ago
- Pan-genome Construction and Population Structure Variation Calling pipeline☆46Sep 13, 2024Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆16Jan 10, 2022Updated 4 years ago
- VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Forma…☆104Aug 27, 2025Updated 7 months ago
- DFOIL: Introgression Testing for Five Taxa☆33May 15, 2021Updated 4 years ago
- Tool for assessing/improving assembly quality in extra-long tandem repeats☆48Feb 23, 2021Updated 5 years ago
- An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.☆151Dec 22, 2025Updated 3 months ago
- Comprehensive, detailed and interactive plots for STRUCTURE and ADMIXTURE population analysis☆24Nov 25, 2024Updated last year
- VCF-kit: Assorted utilities for the variant call format☆134Jul 10, 2025Updated 9 months ago
- ☆12Jun 12, 2023Updated 2 years ago
- Program for aligning DNA sequences, a pairwise aligner.☆243Mar 27, 2026Updated 2 weeks ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- A tool to detect structural variant☆17Mar 27, 2023Updated 3 years ago
- A shiny application to visualize MCscan result☆37Mar 8, 2026Updated last month
- Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085 🟣☆11Apr 28, 2023Updated 2 years ago
- Pipelines for analyzing genomic or transcriptomic data☆17Feb 29, 2024Updated 2 years ago
- Example for TWAS☆12Jan 23, 2022Updated 4 years ago
- Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…☆147Mar 19, 2026Updated 3 weeks ago
- Multi-genome synteny block visualization tool☆55Apr 8, 2026Updated last week
- Scripts to convert between file formats for various analyses☆16May 10, 2025Updated 11 months ago
- A method for variant graph genotyping based on exact alignment of k-mers☆87Apr 1, 2019Updated 7 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 2 years ago
- Code to compute the XP-CLR statistic to infer natural selection☆106Jun 13, 2022Updated 3 years ago
- This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What y…☆11Dec 16, 2022Updated 3 years ago
- A new simple and efficient software to PCA and Cluster For popolation VCF File☆82Jun 25, 2025Updated 9 months ago
- Likelihood-based Selective Sweep Detection☆42Oct 12, 2023Updated 2 years ago
- Scripts to reproduce TrioBinning manuscript☆17Mar 31, 2020Updated 6 years ago
- General tools for genomic analyses.☆389Mar 25, 2026Updated 3 weeks ago