Ident and Sim accepts a group of aligned sequences (in FASTA or GDE format) and calculates the identity and similarity of each sequence pair. Identity and similarity values are often used to assess whether or not two sequences share a common ancestor or function.
Reference:
P. Stothard. The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 2000; 28: 1102, 1104.