Summary of PipMaker and VISTA Server Features
| PipMaker | Both | VISTA | |
| Input files | DNA sequences | ||
| Annotation of the base sequence | |||
| Base sequence mask file | |||
| Underlay files (for any sequence) | |||
| Embedded hyperlink file | |||
| Output files | Alignments in different formats (nucleotide level) | ||
| Ordered and oriented sequence relative to first sequence | |||
| The percent identity plot | VISTA plot | ||
| Dot plot | Conserved sequences | ||
| Analysis of exons: splice junctions, predicted coding sequence | |||
| Limit on the length | ∼2mb, time limited | 4 mb | |
| Implementation | Web server and stand alone programs, finished and draft sequences | ||
| Underlying alignment | Local | Global | |
| Features to be visualized | CpG islands | Genes, exons, repeats, CNSs, order and orientation of aligned sequences | Gaps in both sequences |