Phylogenetics of Brno loanviruses

This is the repository for supplementary materials for the publication

Files:

• 📑 Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
• 📑 dstu_hantavirus_phylo.yaml - conda environment
• 📁 data - data folder:
  • 📑 accession_numbers.txt - list of accession numbers
  • 📑 all_seqs.fa - downloaded sequences
  • 📑 all_seqs_mafft.fa - alligned sequences
  • 📑 accession_organism.txt - list of accession numbers and organisms' names available by that numbers
  • 📑 accession_host.txt - list of accession numbers and names of organisms from which the virus has been isolated
  • 📑 accession_order.txt - list of accession numbers and taxonomic order of organisms from which the virus has been isolated
  • 📑 dataset_for_iTOL.txt - dataset for tree annotation in iTOL
• 📁 model-finder - folder with output files of ModelFinder launch:
  • 📑 tree_MF2.iqtree - main file containing best substitution model
  • 📑 Bunch of log files
• 📁 tree - folder with tree files:
  • 📑 tree_ufb.treefile - unannotated tree
  • 📑 annotated_tree.treefile - annotated tree
  • 📑 Bunch of log files
• 📁 map - folder with the R script to visualize the map

Instruction:

• Create new environment dstu_hantavirus_phylo

conda env create -f dstu_hantavirus_phylo.yaml

Pipeline:

Figure 1. Pipeline overview.

📝 See laboratory journal for more details

Citation

The paper has been published on December 12, 2024 in Brazilian Journal of Microbiology

Ohlopkova, O.V., Stolbunova, K.A., Popov, I.V. et al. Detection of Brno loanvirus (Loanvirus brunaense) in common noctule bats (Nyctalus noctula) in Southern Russia. Braz J Microbiol (2024). https://doi.org/10.1007/s42770-024-01587-5

Full text available here