Hi, I am currently constructing a phylogenetic tree involving heterokonts, specifically of marine diatoms and dinoflagellates. Looking at the BLASTn results of my query sequence, I am wondering which reference sequences should I incorporate. I have been searching for literature on what specific cut off values for percent identity similarity and query cover I should use, however, I noticed that it varies depending on the group of species you're dealing with. I saw one article mentioning that reference sequences with more than 98% similarity indicates phylotype and 97-98% for genus. What cut off values should I use? can you recommend journal articles that can help? Thanks so much
Reference sequences should be from type specimens such as holotype or paratype or epitype reference sequences. GenBank is full or erroneously labeled (unvalidated) sequences. There is no threshold (percent similarity based on BLASTn searches), it is either a type specimen reference or not. When you BLAST your sequence you can select type specimens, which will only return type specimen reference sequences. You may also need to peruse the literature to locate type specimens. Most articles place type sequences in bold or some other notation to indicate type (validated) sequences in a table or phylogenetic tree. Hope this helps!
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