Description: Given two sequences x and y, hCED finds (an approximation of) the cyclic edit distance between x and y.
Installation: To compile hCED, please follow the instructions given in file INSTALL.
hCED <options>
Mandatory arguments:
-i, --input-file <str> (Multi)FASTA input filename.
-o, --output-file <str> Output filename for the rotated sequences.
Optional for Stage 1 (Algorithm saCSC):
-q, --q-length <int> The q-gram length. Default: 5.
-l, --block-length <int> The length of each block. Default: sqrt(seq_len).
Optional for Stage 2 (Refinement):
-P, --refine-blocks <dbl> Refine the alignment of saCSC by
checking P blocks of the ends. Default: 1.
-m, --score-match <int> Score of match for refinement. Default: 1.
-r, --score-mismatch <int> Score of mismatch for refinement. Default: -1.
-f, --score-insertion <int> Score of insertion for refinement. Default: -1.
-g, --score-deletion <int> Score of deletion for refinement. Default: -1.
-O, --gap-open <int> Score of gap opening for refinement. Default: NOT USED.
-E, --gap-extend <int> Score of gap extension for refinement. Default: NOT USED.
Optional for Stage 3 (Edit distance model):
-e, --edit-distance <str> Choose 'Y' to calculate edit distance and 'N' to output
rotation only. Default: Y.
-S, --cost-substitution <int> Cost of substitution. Default: 1.
-I, --cost-insertion <int> Cost of insertion. Default: 1.
-D, --cost-deletion <int> Cost of deletion. Default: 1.
Compute hCED(x,y) and hCED(y,x):
-R, --reverse-computation <int> Choose '0' to compute hCED(x,y) or '1' to compute both hCED(x,y).
and hCED(y,x). Default: 0.
Citation
L. A. K. Ayad, C. Barton, S. P. Pissis, "A faster and more accurate heuristic for cyclic edit distance computation", Pattern Recognition Letters, 2017.
License: GNU GPLv3 License; Copyright (C) 2016 Lorraine A. K. Ayad and Solon P. Pissis