I am new to Ball Python genetics. I have been doing a lot of reading over the last couple of weeks. I am confused about when to refer to something as gene or as an allele. My understanding is that an allele is a variation of the same gene. Terms like recessive and dominant are used to refer to a gene but should it actually be used to refer to an allele? For example a gene might be responsible for tongue colour (the trait). Lets say the normal gene produces a black tongue but a mutated version of the gene produces a yellow tongue. If I have understood anything, the reason the baby ends up with a yellow tongue will be because a) both alleles contained a mutated copy of the gene or b) if the pair of alleles consisted of one normal version of the gene and one mutated version of the gene, the mutated version of the gene was dominant over the normal version of the gene. Does what I’m saying make any sense to anybody or am I going insane?
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Not quite. Terms like recessive and dominant are used to describe the manner in which the mutation is inherited. That said, collectively we do generally use the terms as descriptors of the mutations simply because it is somewhat less cumbersome to say. For example “Albino is recessive” is a bit more fluid in conversation that “Albino behaves as a recessively-inherited morph”
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As I noted above, it refers to the inheritance of the mutation whereas ‘allele’ simply denotes that the variant of the gene in question is different from the WT form. Again, using my example from above: “Albino is recessive” is significantly easier in conversation than “The null allele of the tyr gene behaves as a recessively-inherited morph”
I will also note that an allele does not always denote a mutant phenotype. The redundant nature of the genetic code means that “silent” mutations happen fairly frequently so you can have an allele that, while genetically different from the WT, displays no change in the phenotype of the animal. And as such, you would certainly not be referring to that allele being recessive or dominant
Make sense?
Thank you for taking the time to respond. In answer to your last question, not yet.
Can I bounce another example off you to see where I am off with my understanding?
A gene determines a trait (e.g. eye colour). Locus is the place where the gene for the trait is stored on the strand of DNA. The locus collects one version of the gene from each of the parents. Each individual version of the gene is an allele. These versions of the gene (alleles) could be normal or mutated and could be recessive, dominant or co-dominant. If the two parents both supply a normal copy of the gene and the normal trait is for black eyes, the baby will have black eyes. If one of the parents supply a mutated copy of the gene (for blue eyes) which is recessive in nature, the baby will have black eyes but will be het for blue eyes. If the blue eye version of the gene is dominant in nature the baby will have blue eyes.
I don’t want to think about co-dominant until I am confident that I understand recessive and dominant behaviour first.
You’ve got it right. 
There are way too many places where genetic terminology is used incorrectly, including some within the hobby. Kudos to you for digging to get proper understanding.
As Caryl notes, you mostly have a grip on the situation
The only gentle correction I will give you is that the proper term is incomplete-dominant (inc-dom) and not co-dominant (co-dom). That is one of the major confusion points in the hobby because, as Caryl so rightly pointed out:
Some of the early pioneers in the game did not have a correct understanding and went with what they thought was right and then adamantly refused to accept they were incorrect when actual scientists joined the conversation. To date, there are no confirmed co-dom traits in the hobby