SNP-sites — fast extraction of single nucleotide polymorphism (SNP) sites from multi-FASTA whole-genome alignments. Produces VCF, multi-FASTA (SNP-only), and Phylip output for downstream phylogenetic
Use with AI
Install the MCP server or CLI to instantly fetch SNP-sites documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/snp-sites
docker pull biocontainers/snp-sites:2.5.1BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel
2 shared topics • 2 shared operations
ClonalFrameML detects recombination (horizontal gene transfer) in bacterial whole-genome alignments using maximum likelihood inference. It takes a Newick phylogenetic tree and FASTA/XMFA alignment, th
2 shared topics • 2 shared operations
Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c
2 shared topics • 2 shared operations
OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se
2 shared topics • 2 shared operations
TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a Java-based software package for genome-wide association studies (GWAS), population genetics, and linkage disequilibrium analysis. Su
2 shared topics • 2 shared operations