Discover the application
Once the application is installed on your computer, you can launch it and you will arrive on the home page :
You will then have the choice between three buttons and the 'Dark Mode' button.
On click, this button will allow you to jump on the Genetic window. In this window you will see a description of the steps to follow to create a Genetic Tree from a .fasta file. There is 5 differents pages that are available:
- Get started !: Describe the steps to follow to create a Genetic Tree.
- Fasta File: This page will show you the .fasta file that you have uploaded with the File Browser button.
- Sequence alignment: You need to click on the "Sequence alignment" button to get to this page. In this page you are able to change the alignment method and to lunch it with the Start button. After the sequence alignment is done you can create and visualise the results in the Species Stats and the Genetic Tree pages.
- Species Stats: This page will show the alignment sequence statistic's result. You can change the type of diagrams that you want to plot and you can also change the species name following which one you are interesting in it.
- Genetic Tree: In this page the genetic tree will be plot if the alignment sequence is done. You can select different type of trees to plot.
In this window you will first see a description of the steps to follow to create a Climatic Tree from a .csv file that you have uploaded. There are 4 different pages that are available:
- Get started !: Describe the steps to follow to create a Climatic Tree.
- Climatic Data: When you click on the File Browser button and you upload a .csv file with climatic data, the application will automatically display the Climatic Data page. In this page you will see a tab with the .csv data in it and a map where you can find some points displaying the data locations.
- Climatic Tree: In this page the climatic tree will be plotted. In this page you can select different types of trees to plot.
- Statistics: This page will show some chart types done with the data from the .csv file. You can change the type of chart that you want to plot and you can also change the climate conditions that you want to apply.
This button redirects you into a window where you can visualize the result of the genetic and climatic data compiled with the sequence alignment. The result is a chart with data provided from climatic and genetic data.
The Help button displays a guide about how to use the app and what you need to do to launch the climatic, genetic and results pages.
In the genetic data tab, the user can load a sequence file (only Fasta files are accepted) and align the sequences before generating a phylogenetic tree.
- Select your sequence file in an accepted format (Fasta) through the File browser button.
- Once the file is loaded, the sequence will appear in the main window.
- Launch the sequence alignment through the Sequence Alignment button.
- The sequence alignment process might be CPU demanding so a good PC configuration can be necessary, with an Mac M1 chip, the whole process can take 2 to 3 minutes.
- When the process is done the sequence aligned will be displayed on the main window
- You can create a graph of the species statistics by clicking on the Statistics button.
- Once you are done with the alignment, you can proceed to generate a tree and decide which parameter to create the tree about.
Here is a visual guide to help you:
In the climatic data tab, the user can load a csv file and get a table with the values of the file. A map will be rendered if latitude and longitude values are existing in the said file.
- Select your climatic file in an accepted format (csv) through the File browser button.
- Once the file is loaded, the tab and the map will appear in the main window.
- Click on the Statistics button to generate a graph comparing the different species, based on the parameter you want.
- Once the file is loaded, you can generate a tree by clicking on Climatic Tree
Here is a visual guide to help you:
With both genetic and climatic data we can now move forward to the last section, the Results tab. You can change the settings of the generated results by clicking on the Settings button. The Submit button will generate the results as a table and the Statistics button will create the final tree with the associated parameter.
Here is a visual guide for the result:
