2015-10-19 Martin C. Frith Refactoring.
2015-10-19 Martin C. Frith Refactoring.
2015-10-19 Martin C. Frith Made last-dotplot much faster.
2015-10-07 Martin C. Frith Made last-train handle zero counts more robustly.
2015-10-07 Martin C. Frith Made last-train more likely to find a compatible version of LAST.
2015-10-06 Martin C. Frith Added -s and -m options to last-train.
2015-10-06 Martin C. Frith Small update to tuning doc.
2015-10-05 Martin C. Frith Streamlined the tests.
2015-10-05 Martin C. Frith Added -S option to last-train, and to docs.
2015-10-05 Martin C. Frith Write new lastal option -S in the output header.
2015-10-05 Martin C. Frith Added a test of new lastal option -S.
2015-10-05 Martin C. Frith Added lastal option -S, to control non-strand-symmetric score matrices.
2015-10-05 Martin C. Frith Trivial refactoring.
2015-10-05 Martin C. Frith Refactoring.
2015-10-05 Martin C. Frith Removed unused parameter from lastal output header.
2015-10-05 Martin C. Frith Refactoring.
2015-10-05 Martin C. Frith Refactoring.
2015-10-05 Martin C. Frith Fixed lastal crash with all-zeros score matrix.
2015-10-05 Martin C. Frith Refactoring.
2015-10-05 Martin C. Frith Minor improvements to makefiles.
2015-09-17 Martin C. Frith Made lastdb with option -C (child table) much faster.
2015-09-17 Martin C. Frith Refactoring.
2015-09-17 Martin C. Frith Added NEAR seeding scheme.
2015-09-15 Martin C. Frith Edited the seed & matrix docs a bit.
2015-09-15 Martin C. Frith Enabled setting lastal defaults in lastdb seed files.
2015-09-15 Martin C. Frith Refactoring.
2015-09-14 Martin C. Frith Added YASS built-in seeding scheme.
2015-09-14 Martin C. Frith Added seeding schemes doc.
2015-09-14 Martin C. Frith Enabled setting lastdb options from seed file.
2015-09-14 Martin C. Frith Started implementing lastdb options from seed file.
2015-09-14 Martin C. Frith Made lastdb option -u override -m. Made empty seed patterns errors.
2015-09-14 Martin C. Frith Use at most one lastdb seed file.
2015-09-14 Martin C. Frith Refactoring.
2015-09-14 Martin C. Frith ! Changed the format of subset seed files.
2015-09-14 Martin C. Frith Refactoring.
2015-09-14 Martin C. Frith Made the docs a bit nicer.
2015-09-14 Martin C. Frith Better error message for bad symbol in sequence.
2015-08-31 Martin C. Frith Added MURPHY10 subset seed.
2015-08-31 Martin C. Frith Allow fastq DNA-vs-protein, and non-fastq query vs fastq reference.
2015-08-31 Martin C. Frith Refactoring.
2015-08-31 Martin C. Frith Refactoring.
2015-08-27 Martin C. Frith Refactoring.
2015-08-27 Martin C. Frith Removed a redundant file.
2015-08-27 Martin C. Frith Better error messages.
2015-08-26 Martin C. Frith Added PAM30 matrix.
2015-08-26 Martin C. Frith Added last-matrices doc.
2015-08-26 Martin C. Frith Tried to improve the docs.
2015-08-25 Martin C. Frith Preserve file modification times in the zip.
2015-08-25 Martin C. Frith Refactoring.
2015-08-25 Martin C. Frith Fixed a spelling error (thanks: Charles Plessy).
2015-08-25 Martin C. Frith Increased test coverage.
2015-08-03 Martin C. Frith Doc update.
2015-08-03 Martin C. Frith Minor code cleaning.
2015-06-17 Martin C. Frith Bugfix: lastal expected ins/del counts not quite right with -T1.
2015-06-12 Martin C. Frith Added last-train!
2015-06-12 Martin C. Frith Updated to latest ALP lib: faster E-value calculations at lastal startup.
2015-06-10 Martin C. Frith Bugfix: no E-values for some unusual score parameters since v573.
2015-06-08 Martin C. Frith Made last-split with option --no-split keep expected counts.
2015-06-08 Martin C. Frith Documented lastal expected counts option.
2015-06-08 Martin C. Frith Made lastal non-redundantize gapped alignments more thoroughly.