- 2 Amino aid substitution models 6. - 2.1 Amino aid sequenes and amino aid substitutions. - 2.3 Amino aid substitution models. - 2.4 Methods to estimate amino aid substitution models. - 2.4.2.2 Steps to build an amino aid substitution. - 3 Alignment splitting methods for estimating amino aid. - 3.2 Steps to build an amino aid substitution model by align- ment splitting method. - An Improved General Amino Aid Replaement. - Model of amino aid substitution in proteins enoded. - FLU, an amino aid sub-