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 alignments A and B. If a sequence named "in-A-and-B" is found in both A and B, the spliced alignment will contain a sequence named "in-A-and-B" which represents the characters from A and B joined in direct extension of each other. If a sequence with the name "in-A-not-B" is found in A but not in B, the spliced alignment will contain a sequence named "in-A-not-B". The first part of this sequence will contain the characters from A, but since no sequence information is available from B, a number of gap characters will be added to the end of the sequence corresponding to the number of residues in B. Note, that the function does not require that the individual alignments contain an equal number of sequences.