Patterns / Matrices to be aligned
Pseudo-count (portion) AT-frequency GC-frequency Number of permutations FDR cut-off

Combine Z-score transformed values Use non-transformed values
Kendall's tau Spearman's Pearson's Euclidean Viterbi-score
Hierarchically cluster patterns Pair-wise compare patterns (reports only best matches)
Print pattern clusters at the silhouette level Print all pattern clusters

Substitution score matrix
- A C G T -
A A
C C
G G
T T
Enable spacers Disable spacers
Gap open penalty Gap extension penalty Maximal terminal gap length

Examples


This tool was developed by Matti Kankainen, University of Helsinki and Ari Löytynoja, European Bioinformatics Institute
Contact the Webmaster.
© 2006 University of Helsinki
© 2006 European Bioinformatics Institute