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IMPORTANT
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- 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)
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