ABSTRACT
DNA sequences of different organisms are often related. The closer the species, the more similar are their genomes. Some genes are highly conserved while others have extensive arrangement and mutations. Sequence multiple alignment (msa) help to evidence the relationship between sequences and infer an evolutionary history. There are several programs to perform msa. It is out of the scope of this
book to review them, but there are pointers to several papers in “Additional Resources” for those interested in msa software. One of these programs is muscle (Multiple Sequence alignment by log-
expectation), that is characterized by its improved speed and accuracy over currently available programs. Since muscle has no graphical interface (it is a command line application), we will build a GUI using a web server. The advantage of the use of a web server it is not only the GUI, but the
ability to use it from several computers.
