this answer about the second part secondary structures this is an online service to do so Mfold The mfold web server is one of the oldest web servers in computational molecular biology. It has been in continuous operation since the fall of 1995 when it was introduced at Washington University's School of Medicine. it is so easy and simple for non bioinformation

about the alignment this is also a simple and powerful yet software MEGA is an integrated tool for conducting sequence alignment MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. MEGA is used by biologists in a large number of laboratories for reconstructing the evolutionary histories of species and inferring the extent and nature of selective forces shaping the evolution of genes and species.