This thesis addresses programs and algorithms for multiple alignmentsand models of sequence evolution. The first part of the thesis isabout multiple alignment algorithms and programs in general. Someprograms for multiple alignments are presented. This part alsocontains a presentation of models for nucletide substitution andcodon-substitution models. The other part is a study of how one canuse these models of sequence evolution in a multiple alignment programIttero. Ittero is a program made especially for this thesis. It isused only for coding DNA sequences and because of that, it allows onlygaps that are x times the length of a codon.