9.2 Sequence Alignments

Over evolutionary time, related DNA or amino acid sequences diverge through the accumulation of mutation events such as nucleotide or amino acid substitutions, insertions and deletions.

A sequence alignment is an attempt to determine regions of homology in a set of sequences. It consists of a table with one sequence per row, and with each column containing homologous residues from the different sequences, e.g. residues that are thought to have evolved from a common ancestral nucleotide/amino acid. If it is thought that the ancestral nucleotide/amino acid got lost on the evolutionary path to one descendant sequence, this sequence will show a special gap character “–” in that alignment column.

   9.2.1 Pairwise sequence alignments
    Scoring systems in pairwise alignments
    Algorithms for pairwise alignments
    Pairwise alignment in Geneious Prime
   9.2.2 Multiple sequence alignments
    Progressive pairwise alignment methods
    Multiple sequence alignment in Geneious Prime
   9.2.3 Sequence alignment using ClustalW
   9.2.4 Sequence alignment using MUSCLE
   9.2.5 Other sequence alignment plugins for Geneious Prime
    MAFFT
    Mauve
    LASTZ
   9.2.6 Translation alignment
   9.2.7 Combining alignments and adding sequences to alignments