Start whit aligment existent and newick file

hi , im working with 7000 sequences in aminoacids format of only one gene(pretein E-length: 495Aas) im trying to do analysis starting a aligment file and newick file, rigth now i buit a metadata file, and the output.gb files, what is the following that i have to do for meke correctly this instructive https://nextstrain.org/docs/tutorials/zika