Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalo / TODO

diff --git a/website/archive/binaries/mac/src/clustalo/TODO b/website/archive/binaries/mac/src/clustalo/TODO
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-IMPORTANT
----------
-
-- consensus output (sto,aln) and compatibilety with bioperl/biopython
-
-- Split Homfam refs in two. Use one part as background HMM, the other parts
-  for benchmarking
-
-- Implement meta flags:
-  accurate: --iterations 3
-  default:  --mbed --iterations 1
-  fast: --mbed
-  and for more than 10k sequences: --mbed --mbed-iter
-
-- SSE instructions for hhalign (little use in ClustalO frontend; DD)
-  /
-  Patch new code which already contains SSE instructions
-
-  also fix automake/configure then
-
-- Multi-HMMs; also for Pfam+iteration (FS)
-
-- Show degradation of alignment quality when using x reference sequences
-  added to y random/false sequences
-  (Lio Pachter)
-
-- Seed pre-alignment with M-Coffee, MSAProbs, ...
-
-- GUI/API:
-  Will have to catch/override exits from source.
-  find . -name \*.c -or -name \*.cpp -or -name \*.h | xargs grep 'exit('
-  Also best to allow for user override of
-  void Fatal(char *msg, ...);
-  void Error(char *msg, ...);
-  void Warn(char *msg, ...);
-  void Info(int level, char *msg, ...);
-
-
-- Soeding: DNA/RNA alignment incl. reading of nucleotide HMMs
-
-- Automatic HMM-selection/search/download for input
-
-- Structure input: Psipred predictions are apparently part of their
-  hhms and should therefore be ready to use (part automatic
-  HMM-selection)