You have at least two options for your final project. One is to do a project that involves software development, either to produce a new method and study it, or to compare existing methods. The other main option is to do a survey paper on some topic related to phylogenetic analysis and multiple sequence alignment. Of these two basic categories, the survey paper is much easier, but the first category is much more fun!
There are journals that you can consider submitting a research paper to, including PLoS Currents, Tree of Life, see here. The advantage of PLoS Currents is that the requirements for acceptance do not focus on perceived impact (where reviewers can disagree substantially). It is not required that you submit your research paper to a journal, however!