This repository contains sequence alignments and scripts used in the paper.
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There are 5 sequence alignments, which were used in the paper. full_alignment.fasta includes all sequences of TBEV available on 11.04.2018 at Genbank database. This alignment includes sequences with Genbank IDs EF469661 and MF774565, which were excluded from the later analysis. for_GS_analysis.SSE alignment was used for the GS analysis. It already contains sequences divided into 4 groups used in the analysis: Siberian, Far-Eastern, OHFV, European. Sequences from 886-84-like group are represented by the consensus sequence on which the analysis was done. Finally, allignments of JCFs JCF1_2329-3388.fasta, JCF2_5520_5770.fasta, JCF2_6640-6970.fasta, JCF3_7810-8160.fasta contain were used for the Bayesian reconstruction of the conflicting phylogeny characteristic for recombination. NB: full_alignment.fasta has fully corrected labels for sequences, containing only the genotype and Genbank ID. Sequences in other alignment are not yet redacted accordingly, this will be done in due time.
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Folder reshuffling contains python scripts used for the GSAUC analysis and its visualisation. For these scripts to work you have primarily to install SSE software (limitied to Windows OS) together with Phylip library to enable GS analysis. Next, you have to install pywinauto package on top of python3, used for automatisation of the GSAUC analysis. Pay attention to the version of pywinauto used in the analysis (v. 0.6.5), novel versions may not be compatible with the scripts. Scripts will likely not work on locked machines. You should either disable auto-locking of your local pc, or you may try improving script according to the guide: https://pywinauto.readthedocs.io/en/latest/remote_execution.html
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Folder visualisation contain an ipynb notebook, which was developed to process and visualise GSAUC analysis results. To launch the visualisation script you have to provide 3 arguments: path_to_file, path_to_folder, path_to_save. To reproduce the analysis download the zip-archive from here, unpack it. As path_to_file provide "path_to_unpacked_folder/ref_scan_250_40.DAT", path_to_folder - "path_to_unpacked_folder/scans", path_to_save - where you want to output images.