4 - consensus output (sto,aln) and compatibilety with bioperl/biopython
6 - Split Homfam refs in two. Use one part as background HMM, the other parts
9 - Implement meta flags:
10 accurate: --iterations 3
11 default: --mbed --iterations 1
13 and for more than 10k sequences: --mbed --mbed-iter
15 - SSE instructions for hhalign (little use in ClustalO frontend; DD)
17 Patch new code which already contains SSE instructions
19 also fix automake/configure then
21 - Multi-HMMs; also for Pfam+iteration (FS)
23 - Show degradation of alignment quality when using x reference sequences
24 added to y random/false sequences
27 - Seed pre-alignment with M-Coffee, MSAProbs, ...
30 Will have to catch/override exits from source.
31 find . -name \*.c -or -name \*.cpp -or -name \*.h | xargs grep 'exit('
32 Also best to allow for user override of
33 void Fatal(char *msg, ...);
34 void Error(char *msg, ...);
35 void Warn(char *msg, ...);
36 void Info(int level, char *msg, ...);
39 - Soeding: DNA/RNA alignment incl. reading of nucleotide HMMs
41 - Automatic HMM-selection/search/download for input
43 - Structure input: Psipred predictions are apparently part of their
44 hhms and should therefore be ready to use (part automatic