Phylogenetics of Alphacoronaviruses

This is the repository for supplementary materials for the publication

Directories:

📁 01_Phylogenetics - phylogenetic analysis
📁 02_Seqs_identity - nucleotide sequences identity analysis
📁 03_Map - phylogeographic analysis
📁 04_Primers - PCR primers selectivity analysis

Instruction:

Create new environment phoacr

conda env create -f phoacr.yaml

Pipeline:

Figure 1. Pipeline overview.

System

OS: Ubuntu 22.04 (WSL2 on Windows 11 22H2)
RAM: 32GB (16 for WSL2)
CPU: Intel Xeon E5-2670v3

Citation

The paper has been published on December 29, 2024 in Microbiology Research

Ohlopkova, O.V.; Popov, I.V.; Popov, I.V.; Stolbunova, K.A.; Stepanyuk, M.A.; Moshkin, A.D.; Maslov, A.A.; Sobolev, I.A.; Malinovkin, A.V.; Tkacheva, E.V.; et al. Detection and Phylogenetic Analysis of Alphacoronaviruses in Bat Populations of Rostov and Novosibirsk Regions of Russia, 2021–2023. Microbiol. Res. 2025, 16, 3. https://doi.org/10.3390/microbiolres16010003