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

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

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

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.