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| [[GPL]]
| [http://www.red-bean.com/ale/ link]
|-
| Base-By-Base
| No
| Muscle
| UPGMA, NJ, Complete Linkage, Single Linkage, WPMGA
| Visual summary, percent identity tables, some integrated advanced analysis tools
| Genbank, Fasta, EMBEL, Clustal, Base-by-base files
| Free, registration required
| [http://athena.bioc.uvic.ca/virology-ca-tools/base-by-base/ link]
|-
| BioEdit
|