Starting with tag: [TAG 0.2 Ketil Malde **20061017135853] [simple N-W impl Ketil Malde **20061129132539] [generalized NW/SW alignment Ketil Malde **20061130111955] [factored out matrix construction Ketil Malde **20061130112023] [showalign function Ketil Malde **20061130112037] [rename backtrack Ketil Malde **20061130112525] [renamed nw-specific backtracking Ketil Malde **20061130142656] [generalized backtracking Ketil Malde **20061130142734] [docs and type sigs Ketil Malde **20061130151614] [generalized backtracking to cover local alignments, too Ketil Malde **20061130155243] [refactor, and add affine scores Ketil Malde **20061201092533] [factored things more finely Ketil Malde **20061204122309] [commented out non-functioning affine scoring Ketil Malde **20061204122333] [almost-working columnwise version Ketil Malde **20061204152643] [fix pesky off-by-one bug Ketil Malde **20061205083625] [qc property Ketil Malde **20061205083641] [no need to be so grumpy about unfoldr Ketil Malde **20061205083739] [Needs glasgow-exts for parallel list comprehension Ketil Malde **20061205124906] [loosen type for mkcolumns (why isn't mkcol's sig accepted?) Ketil Malde **20061205124924] [proper QC properties Ketil Malde **20061205125153] [simpler arbitrary Char, commented-out failing test testing test Ketil Malde **20061205130158] [simplified arb instance for Char Ketil Malde **20061205141329] [substitution matrices supported (and checked) Ketil Malde **20061205141341] [doc additions Ketil Malde **20061205141538] [type decl fix (thanks, dons) Ketil Malde **20061206091417] [proper hierarchical module name Ketil Malde **20061206132305] [big reorganization of everything in AlignBase Ketil Malde **20061206144540] [latex preamble/end Ketil Malde **20061206145413] [reorganized the scoring function stuff Ketil Malde **20061207134203] [quickcheck stuff Ketil Malde **20061207134316] [direct recursion for illustration purposes only Ketil Malde **20061207134344] [linear space score calculation Ketil Malde **20061207134400] [minor doc/comment/latex fixes Ketil Malde **20061207134415] [moved QC defs earlier in the file Ketil Malde **20061208125429] [parametrize columns by hd/tl Ketil Malde **20061208125451] [added parametrized reversal of sequences Ketil Malde **20061208125514] [rephrasing and cabal resolution Ketil Malde **20061211085624] [comment added Ketil Malde **20061211135442] [generalized qc_align and bug fix Ketil Malde **20061211135550] [added iterative linear space algorithm Ketil Malde **20061211135611] [separate tabulate - simpler, but uses more memory(?) Ketil Malde **20061214110240] [mod to qc prop Ketil Malde **20070208092628] [reorg seqdata, added 2bit format (read only for now) Ketil Malde **20070208092659] [read2bit works - yay! Ketil Malde **20070208195554] [factored out decoding function Ketil Malde **20070212102131] [comment fix, reshuffling Ketil Malde **20070221090749] [fix: negative numbers didn't work out so well, be positive instead Ketil Malde **20070221090840] [partially implemented parser for BLAST output Ketil Malde **20070307153445] [QC and a property ketil@malde.org**20070308094303] [put impl for SRLE ketil@malde.org**20070308094331] [set glasgow-exts for Fasta.hs Ketil Malde **20070308094609] [added sequence metamodule Ketil Malde **20070308095036] [moved alignment stuff to separate directory Ketil Malde **20070308121608] [blast working - but chunk parsing missing Ketil Malde **20070308122422] [moved to ByteStrings Ketil Malde **20070309090113] [modified data structures, debugging reads Ketil Malde **20070309224316] [remove commented-out code Ketil Malde **20070314112724] [section header for gapped (unfinished) Ketil Malde **20070314112736] [added (untested) rcpacked for 454 sequences Ketil Malde **20070315123430] [protect against older formats (blast ver. 2.2.13 puts db inside each record) Ketil Malde **20070315143733] [Added some QC tests Ketil Malde **20070316123714] [QC for rcontig Ketil Malde **20070319103212] [added debian infrastructure Ketil Malde **20070320124823] [export most stuff through Sequence.hs (cf. bio-0.3 patch for RBR) Ketil Malde **20070323101126] [updates to compile against ghc-6.4.2 Ketil Malde **20070323125330] [(had)doc(k) fixes and additions Ketil Malde **20070323143725] [added amino translation stuff Ketil Malde **20070420200114] [Add Xxx amino, trans1 no longer maybe Ketil Malde **20070422194429] [added IUPAC stuff for proteins Ketil Malde **20070423205814] [fix for RNA, commments Ketil Malde **20070423210511] [Xaa not Xxx, added Xle Ketil Malde **20070423211511] [export IUPAC funcs, comment typo fix Ketil Malde **20070510133626] [warn fix Ketil Malde **20070511132558] [added phd support Ketil Malde **20070511132631] [support quality info for Sequences Ketil Malde **20070511132714] [output qual files Ketil Malde **20070518083104] [strictness fix(?) Ketil Malde **20070522220824] [Simple README added Ketil Malde **20070522220837] [major documentation overhaul - some export mods Ketil Malde **20070524130759] [export hashword stuff Ketil Malde **20070524133131]