For citation please use this paper:

Deviatkin AA, Vakulenko YA, Dashian MA, Lukashev AN. Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses. Viruses. 2022; 14(1):66. https://doi.org/10.3390/v14010066

This application is implemented on the shinyapps.io platform for demonstration of its possibilities ( https://andreideviatkin.shinyapps.io/gene-geo/ ). However, free plan on this platform has some computational limitations.

To run this application on personal computer please complete the following steps:

1. Install R (Version 4.0 or above)

https://cran.r-project.org/bin/windows/base/

2. Install Rstudio.

https://www.rstudio.com/products/rstudio/

3. Download all files from

https://github.com/AndreiDeviatkin/gene_geo

into separate folder.

Open the file 'packages_installation.R' in Rstudio -> select all lines -> click on 'Run' button at topright corner of the console. Packages needed for the application running will be installed.

Open the file 'ui.R' in Rstudio -> click on 'Run App' button at topright corner of the console. The application will begin to process your task.

If you have any problems while using 'Gene-geo' please don't hesitate to contact me,

andreideviatkin@gmail.com

kind regards,

Andrei

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This application needs two files:

1. Fasta alignment

Fasta descriptor (symbols after '>') must contain information about place of virus collection

Separator in fasta descriptor should be '_'

Place of virus collection should be located at the last place

Fasta descriptor example: '>AY352458_isolate_857r_country_Russia-Khabarovsk'

Fasta file example:

https://raw.githubusercontent.com/AndreiDeviatkin/gene_geo/main/data/fasta/arctic-like_geo_natural.fas

2. text file with coordinates of geographic regions

One line example: REGION,LAT_LONG

File example:

https://raw.githubusercontent.com/AndreiDeviatkin/gene_geo/main/data/regions_coordinates/regions_coord.txt