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NGPhylogeny.fr : galaxy

This repository contains tools and workflows used in NGPhylogeny.fr.

Tools

Wrappers for several phylogenetic tools are defined:

  • Mutliple alignment:
    • Clustal Omega
    • MAFFT
    • Muscle
    • Noisy
  • Alignment curation:
    • BMGE
    • Gblocks
  • Tree inference:
    • FastME
    • FastTree
    • MrBayes
    • PhyML
    • PhyML-SMS
    • TNT
  • Others
    • goalign
    • Newick Utilities

Workflows

Using these tools, several workflows are defined:

  • FastME OneClick: Complete workflow using FastME
  • FastTree OneClick: Complete workflow using FastTree
  • PhyML-SMS OneClick: Complete workflow using PhyML-SMS
  • PhyML OneClick: Complete workflow using PhyML

Galaxy instance

To test these galaxy tools and workflows, you can use the docker image automatically built on docker hub:

docker run --privileged=true \
           -p 8080:80 \
		   -p 8121:21 \
		   -p 8122:22 \
		   evolbioinfo/ngphylogeny-galaxy

This image integrates a running galaxy instance, with all phylogenetic tools installed on environment modules using singularity images.