Navigating The Website - EvidentialGene Part 1

    Note: The following few posts on this project are not in real-time, but are separated into parts so that I can show how I progressed chronologically; i.e., I didn't blog this project while I was doing it.

    Disclaimer: Please do not take anything I say in these posts as professional advice and/or criticism. I do not have a higher education degree in the topics I'll be indulging in the next few posts.

    My plan going into this was to simply use EvidentialGene to magically join together two genome assemblies. This was not the case. At least, not the simple and magical part.

    The system I've done all this on is running Ubuntu 22.04 LTS. I think it's a reasonable choice since there isn't much bloatware, and I can easily run things from the terminal. Getting to the website with my goal in mind, I came upon a confusing sight. It's not very user-friendly in my opinion, but then again this was my first time using something akin to it. After some digging, I figured out that I'd need to use the tr2aacds pipeline to combine my assemblies together. I gleaned quite a bit of the info to come to this conclusion from these links: 

• the About page for Evigene, http://arthropods.eugenes.org/EvidentialGene/evigene/
• the blog/discussion page for Evigene on SourceForge, https://sourceforge.net/p/evidentialgene/blog/
• this video where Don Gilbert (developer of EvidentialGene) speaks on the program, https://www.youtube.com/watch?v=Lu4JqZPGKW0&ab_channel=IUPTI

    These links helped me out a lot, especially the SourceForge blog one. The About page is a little hard to learn from since the formatting and organization of topics are hard to follow in my opinion, but regardless, it is a valuable source of information. 

    Next, I needed to get the proprietary software for tr2aacds to work. These are:

(from the About page)

This part of getting all the proprietary software proved to be a bit of a hassle, as will be evident in the later posts. Thankfully a test case is provided that helps in the troubleshooting phase.