Sydney Phylo Workshop by Simon Ho provides some excellent lecture notes and workshops with dataset
Phylogenetic Biology by Casey Dunn at Brown University is a great source of lecture and practical material. It also has a an extensive list of extra resources and useful links to reading material
RevBayes github page has a wealth of information specifically around the software but also includes some general phylogenetics material as well. Tutorial pages available here, a example of workshop page on molecular phylogenetics and fossil data available here
Taming the BEAST workshops around the use of BEAST software for Phylogenetics
Decide on appropriate method and model - this will differ depending on your study question, data available, gene(s), length of sequence, type of data (i.e. nucleotide, amino acid etc)
You will likely need to use some program to help you decide on most appropriate model
Conduct phylogeny recontsruction (with or without bootstrap/node support)