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 - 📁
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 theR
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