How alignments are joined

Alignments are joined by considering the sequence names in the individual alignments. If two sequences from different alignments have identical names, they are considered to have the same origin and are thus joined. Consider the joining of the alignments shown in figure 13.15 "Alignment of isolates_abcZ", "Alignment of isolates_aroE", "Alignment of isolates_adk" etc. If a sequence with the same name is found in the different alignments (in this case the name of the isolates: Isolate 1, Isolate 2, Isolate 3, Isolate 4, and Isolate 5), a joined alignment will exist for each sequence name. In the joined alignment the selected alignments will be fused with each other in the order they were selected (in this case the seven different genes from the five bacterial isolates). Note that annotations have been added to each individual sequence before aligning the isolates for one gene at the time in order to make it clear which sequences were fused to each other.