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 # Synyin Deed
- 
+
+# General
+Synteny Index (SI) is a newly-developed method for genetic alignment of organisms. It has been proved to be more accurate (in certain conditions) than sequence-based approaches. That is, for prokaryotes (Bacteria & Archea).
+I've been developing Syntin Deed as part of a study, which undermines to find out whether SI is also as good for eukaryotes (All other organisms) genetic comparisons.
+
+# How to use?
+Download the program to your desktop and run "run.bat".
+You should see something like this:
+![image](https://user-images.githubusercontent.com/73846269/204306416-6f4aa33d-788f-4668-8efd-a5bb5990e801.png)
+
+"Covnert" and "Analyze" are essentials. The rest are quality-of-life functions.
+Press the number of category of commands that you want to choose. For example: Enter '1' to enter the "Convert" category.
+
+
+1. Convert:
+
+![image](https://user-images.githubusercontent.com/73846269/204307786-125b1b04-93a2-47c3-bad6-d4785434b947.png)
+
+1. GFF3 & FASTA -> GENELIST2: This is the first essential command. A .genelist2 file is a special type of file that you can then apply the SI algorithm to.
+This function takes 4 files: The GFF and FASTA of each genome. Put those of the first genome in Main_Input/File 1 and those of the second one in Main_Input/File 2, then choose this command in console.
+
+Output:
+All output files are generated in Main_Output folder.
+
+
+# Further Reading
+https://www.sciencedirect.com/science/article/pii/S1055790318303087?casa_token=by3jqQtFBGkAAAAA:3cTVYapeSlpMskMnUAtWrLXgZej8BnTzTVLnqRDD8rQLI_OyPohnS4gVz2NGjmJP5evNGClh3A