ELIXIR Belgium
Web page: https://www.elixir-belgium.org/
Funding details: Related items
Teams: GalaxyProject SARS-CoV-2, usegalaxy.be workflows, EuroScienceGateway
Organizations: ELIXIR Belgium, VIB
https://orcid.org/0000-0001-6565-5145
Teams: usegalaxy.be workflows
Organizations: ELIXIR Belgium
Teams: ELIXIR Belgium, usegalaxy.be workflows
Organizations: ELIXIR Belgium
https://orcid.org/0000-0001-7461-1427
Galaxy workflows developed by ELIXIR Belgium team.
Space: ELIXIR Belgium
Public web page: https://usegalaxy.be/workflows/list_published
Phylogenetic reconstruction using genome-wide and single-gene alignment data. Here we use maximum likelihood reconstruction program IQTree. Data can be prepared using the phylogenetic data preparation workflow prior to phylogenetic reconstruction. Resulting trees can be viewed interactively using Galaxy's 'Phyloviz' or 'Phylogenetic Tree Visualization'
This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. Test dataset: https://zenodo.org/record/6610704#.Ypn3FzlBw5k
