Phylogenetics of Brno loanviruses

This is the repository for supplementary materials for the upcoming publication

Files:

• Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
• dstu_hantavirus_phylo.yaml - conda environment
• geo-map.R - R script to draw phylogeography plot
• 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

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