PhyloProfile

PhyloProfile is a software tool to visualize using R Shiny and investigate multi-layered phylogenetic profiles. The PhyloProfile package can display presence and absence patterns of orthologs, sequence similarity, and domain architecture among orthologs, dynamic filtering of profiles, and estimate the age of genes and differences in functional annotations. The PhyloProfile uses NCBI taxonomy to collapse systematics groups.

Topic

Phylogenetics;Data visualisation;Genetics

Detail

  • Operation: Phylogenetic tree visualisation;Phylogenetic tree generation;Phylogenetic tree analysis

  • Software interface: Graphical user interface

  • Language: R

  • License: The MIT licence

  • Cost: Free

  • Version name: 1.8.0

  • Credit: Deutsche Forschungsgemeinschaft

  • Input: FASTA, tab-separated file, OMA ID, Ortho XML

  • Output: -

  • Contact: Vinh Tran tran@bio.uni-frankfurt.de

  • Collection: -

  • Maturity: Stable

Publications

  • PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles.
  • Tran NV, Greshake Tzovaras B, Ebersberger I (2018). PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles. Bioinformatics 34(17): 3041-3043.
  • https://doi.org/10.1093/bioinformatics/bty225
  • PMID: 29659708
  • PMC: -

Download and documentation

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