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Use when building phylogenetic trees from genomic sequences using minimap2 for all-vs-all alignment and pairwise distance computation. Covers minimap2 PAF output, distance matrix construction, tree in
Use with AI
Install the MCP server or CLI to instantly fetch minimap2-Based Phylogenetics documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/minimap2-based-phylo
Use when classifying plant protein sequences into gene families, estimating gene family evolution, or performing phylogenomic analysis with PlantTribes2. Covers scaffold-based gene family classificati
2 shared topics • 2 shared operations
BEAST2 — 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 • 1 shared operation
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 • 1 shared operation
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 • 1 shared operation
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 • 1 shared operation