I apologize for the question, I'm quite the beginner with bioinformatics. Im not quite sure which fasta file to choose in NCBI for the phylogenetic analysis of beta casein of different animals. Thank you.
I don't know what the LJ.8 means. You can search the NCBI Gene database for "beta casein capra hircus". That will bring up goat (capra hircus) CSN2. Clicking that link will bring up a lot of information, but you can scroll down to "NCBI Reference Sequences (RefSeq)" , "mRNA and Protein(s)". Then click on XM_005681721.2 for isoform X1. "CDS" then gives you the translated amino acid sequence, and "ORIGIN" gives you the DNA sequence. You can follow the same steps for any species. Hope this helps.
You can search the NCBI Gene database for CSN2. Then click on the link for your species of interest. You can then scroll down to the NCBI Reference Sequences (RefSeq) section. Using mouse as an example, there is a subsection called Genomic that includes a FASTA sequence. You can then repeat this for all of your species of interest.
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LJ.8 has no relevant meaning except as a strain identifier. It could be initials of the person who isolated it followed by a strain number, or it could be something altogether different.