Dear XXXXXX,

i finally found some scripts and some models used (not lost 8 years after ... i'm quite lucky !! But i also found some bugs :-/ )

i put them here :
    http://bioinfo.lifl.fr/yass/hedera_unifyingframework/

- there are four models : 
    B.txt M3.txt M13.txt and HMM.txt
- there is a script (now set to loop only on the last model HMM.txt )
    run_Hedera.pl

but i prefers the command line to check first ... and as you mentionned, everything seems "not so" good ...

(A) i tried the Table 2 first line (weight 9) experiments :
    http://www.lifl.fr/~noe/files/pp_JBCB06_preprint.pdf
(i have not access to my final paper ... so i dont know if something different was provided :-( )

    ./hedera -P 0.170329896325393,0.19864551411205,0.631024589562557  -W 9,9 -S 9,16
    # Match Prob     Seed()s
    0.443276    ###___#_#_##_##    

... same seed as in the paper, but not same sensitivity (??)

    ./hedera -P 0.170329896325393,0.19864551411205,0.631024589562557  -W 9,9 -S 9,16 -T 2,2
    # Match Prob     Seed()s
    0.469798    ###_#__#@#_@##

... same seed as in the paper, but not same sensitivity (??)

=> Conclusion 1: there is something wrong here !! and you are the first one to get this ... "chapeau bas" (hats off ?)

 (B) i also tried Table 3 and Table 4 first line (weight 9) to see if this bug was all the same here too :

In Table 3 :

    ./hedera -P 0.239787075656607,0.294514985108333,0.46569793923506,0.135102832385977,0.152643232489794,0.712253935124229,0.136156297472795,0.148850010202096,0.714993692325109 -W 9,9 -S 10,16
    # Match Prob     Seed()s
    0.51208    #_##____##_##_##

    ./hedera -P 0.239787075656607,0.294514985108333,0.46569793923506,0.135102832385977,0.152643232489794,0.712253935124229,0.136156297472795,0.148850010202096,0.714993692325109 -W 9,9 -S 10,16 -T 2,2
    # Match Prob     Seed()s
    0.532289    #_#@_##_@__##_##

the results look like the results of table 4... and not table 3.

In Table 4 :

    ./hedera -P 0.0108914311141944,0.0132938253706108,0.0131124554258471,0.0110738110745614,0.00924207563400844,0.0114443425130285,0.0188732958511733,0.0194566520060497,0.0310627413035492,0.0102249651039609,0.00983567623286112,0.0109290902674031,0.00955619048663417,0.0102526683890799,0.0129408970612297,0.0215455085616137,0.0255171784896688,0.0398327067869874,0.0208276760435553,0.0215752318779393,0.0255447374868445,0.025368273332154,0.0260416651636673,0.0377675134541293,0.112984096871462,0.161659490265325,0.279145803832461 -W 9,9 -S 9,16 ;
     # Match Prob     Seed()s
     0.609241    ##_##_##____##_#    
    ./hedera -P
0.0108914311141944,0.0132938253706108,0.0131124554258471,0.0110738110745614,0.00924207563400844,0.0114443425130285,0.0188732958511733,0.0194566520060497,0.0310627413035492,0.0102249651039609,0.00983567623286112,0.0109290902674031,0.00955619048663417,0.0102526683890799,0.0129408970612297,0.0215455085616137,0.0255171784896688,0.0398327067869874,0.0208276760435553,0.0215752318779393,0.0255447374868445,0.025368273332154,0.0260416651636673,0.0377675134541293,0.112984096871462,0.161659490265325,0.279145803832461 -W 9,9 -S 9,16 -T 2,2
     # Match Prob     Seed()s
     0.620041    ##@##_##____##_@  

=> Conclusion 2: i made a mistake here too : reversing Table 3 and Table 4 and "current paper" Table 3 has the same bug as Table 2 (Conclusion 1) !!

 (C) i also tried Table 5  :
    ./hedera -P   
 0.905262722040495,0.0947372779595048,0,0,0.179893948360603,0.696267771359667,0.12383828027973,0,0,0.21314702706083,0.695852484684932,0.0910004882542386,0.0699249318123762,0.0412929966572271,0.128688517835905,0.760093553694492,0.0157690008627721,0.0174226965015032,0.0143950436244674,0.0151052847000763,0.0121524250374702,0.0113526676737249,0.025023336071825,0.0235257050143844,0.0278554665300365,0.0147819660014782,0.0136453447113247,0.0126612544647721,0.0134769127481206,0.0132407546458659,0.0134574782908278,0.0281511058500661,0.0298136353330212,0.0344249020179445,0.027010951022223,0.0283790190310451,0.0259997703200502,0.0342894497398433,0.031575103871285,0.0340562362523299,0.129728535966997,0.174616243083836,0.178089710632709,0.00962225802620463,0.0124076485074744,0.015011529230914,0.00891414588454635,0.00752705279693092,0.0124703926212922,0.0179134444949883,0.0184109156831153,0.0352958048837329,0.00817690254718693,0.00766150446939768,0.0111527662311179,0.00738363767963304,0.00952141927185456,0.0135348016949874,0.0182809457330641,0.0297810454513879,0.0440463679001114,0.0194573978671483,0.0168154225031764,0.02344164909458,0.0245553571148464,0.0266841752622368,0.0389035914282577,0.121129752586514,0.181695749310375,0.260204321724925,0.00405727238816677,0.00691515308025595,0.00953774640612895,0.00500989928552983,0.00372442684571461,0.00840721930504146,0.0103354279647643,0.0112880548621273,0.0343003070213193,0.00391380448193739,0.00395971421193079,0.00757510544891108,0.00363834610197699,0.00707009841898367,0.0147312846116324,0.0128776792631488,0.0197469226134114,0.0505753063039798,0.0125046627069525,0.0162692605664113,0.024159995409027,0.0141861065679607,0.0207110269432728,0.0442741958623856,0.100140598548105,0.153108949527991,0.396981435252934,0.00301872463630538,0.00267460901345611,0.005600778413271,0.00289294444312599,0.00249187175166718,0.00806891805301754,0.00740441891923962,0.00709827467546337,0.0319481690675653,0.00296651399007998,0.00260815910007832,0.00355269715451978,0.00298549967961649,0.002707833970145,0.00934807888554002,0.00924365759308921,0.0114815957472055,0.0429622422099343,0.010347200797399,0.0112513942615753,0.0220376391295061,0.00929824145050668,0.0128889099840995,0.0423523269335738,0.0530388969314379,0.0816289721622327,0.598101431046349 -W 9,9 -S 9,16
    # Match Prob     Seed()s
    0.525255    ##_##_##____##_#

this one seems OK !!

=> Last Conclusion  : finishing a PhD thesis and a paper at the same time is not good for the paper ...

Laurent