apex is an R tool for use in phylogenetics to handle, analyze, store, and visualize DNA and amino acid sequence data.


Phylogenetics;Statistics and probability;Data architecture, analysis and design


  • Operation: Sorting

  • Software interface: Command-line user interface

  • Language: R

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.0.4

  • Credit: The Medical Research Council Centre for Outbreak Analysis, the National Institute for Health Research – Health Protection Research Unit (NIHR HPRU) in Modelling Methodology at Imperial College London in partnership with Public Health England, the National Science Foundation, United States Department of Agriculture (USDA) Agricultural Research Service (ARS), USDA Animal and Plant Health Inspection Service, the USDA‐ARS Floriculture Nursery Initiative, the Oregon Department of Agriculture-Oregon Association of Nurseries, the USDA Forest Service Forest Health Monitoring Program.

  • Input: FASTA

  • Output: -

  • Contact: Klaus Schliep thibautjombart@gmail.com, Klaus Schliep klaus.schliep@umb.edu

  • Collection: -

  • Maturity: Stable


  • apex: phylogenetics with multiple genes.
  • Jombart T, Archer F, Schliep K, Kamvar Z, Harris R, Paradis E, Goudet J, Lapp H. apex: phylogenetics with multiple genes. Mol Ecol Resour. 2017 Jan;17(1):19-26. doi: 10.1111/1755-0998.12567. Epub 2016 Aug 12. PMID: 27417145; PMCID: PMC5215480.
  • https://doi.org/10.1111/1755-0998.12567
  • PMID: 27417145
  • PMC: PMC5215480

Download and documentation

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