Progressive alignment of amino acid sequences and construction of phylogenetic trees from them.

Publisher Summary This chapter discusses the progressive alignment of amino acid sequences and construction of phylogenetic trees from them and a much improved, easier to use, set of programs, which is refer to as ProPack––a packet of programs centering on progressive alignment. The changes pertain mainly to speeding up the calculations and reducing the number of manual operations; the basic idea of progressive alignment remains the same. The principal new features of ProPack are introduction of an option for choosing an alternative amino acid substitution matrix, automatic elimination of negative branch lengths in the calculation of phylogenetic trees, addition of a bootstrap analysis option, and inclusion of a simple program for converting output to a form that can be used to draw trees on a microcomputer with standard software. The bootstrapping is restricted to solutions with no negative branch lengths, a necessary condition if the likelihoods are to have any meaning.