Program name | Description |
alignrunner | Runs alignment program on all sequence pairs in a directory |
contactalign | EMBOSS implementation of Damian Counsell's 2.5-D alignment algorithm |
esim4 | Align an mRNA to a genomic DNA sequence |
est2genome | Align EST and genomic DNA sequences |
nawalign | Damian Counsell's implementation for protein sequences of the Needleman and Wunsch alignment algorithm |
nawalignrunner | Runs nawalign alignment program on all sequence pairs in a directory |
needle | Needleman-Wunsch global alignment |
needlerunner | Runs needle alignment program on all sequence pairs in a directory |
scorer | Scores accuracy of protein-protein sequence alignment against gold standard structure-structure alignment |
scorerrunner | Runs scorer to compare ordered pairs of substituted seqs in two directories and write the scores to a third |
stretcher | Finds the best global alignment between two sequences |
substitute | Substitutes matches from first (query) sequence of two aligned sequences in a trace into second (template sequence) |