The following prediction is included as an example of the output from Jnet v0.1, other output formats are available, see the documentation:

[james@slug src]$ ./jnet -p ../examples/1add.fa ../examples/1add.msf.hmmprof ../examples/1add.blast.pssm ../examples/1add.blast.freq
MODE: Prediction
JNet Started!
Reading Data
There are 7 sequence homologues in the file
Generating...
        Length numbers
        Profile - frequency based 
        Profile - average mutation score based 
        Conservation numbers
Done initial calculations!

Found HMM profile file...
Using HMM enhanced neural networks

Found PSIBlast profile files...
Using PSIBlast enhanced neural networks

Running final predictions!

Both PSIBLAST and HMM profiles were found
Accuracy will average 76.4%

Length = 349 Homologues = 7
 RES    : TPAFNKPKVELHVHLDGAIKPETILYFGKKRGIALPADTVEELRNIIGMDKPLSLPGFLAKFDYY 
 ALIGN  : ----------H----------HHHHHH---------------------------HHHHHHHHHHH 
 HMM    : --------HHHHHH------HHHHHH----------H------------------HHHHHHHHHH 
 FREQ   : ---------EEEE-------HHHHHHHHHHH--------HHHHHHHHH---------HHHHHHHH 
 PSSM   : ---------EEE--------HHHHHHHH------------HHHHH-HE-------HHHHH----- 
 CONF   : 87766772000002354544437877741317878847624433345204787634612175236 
 NOJURY :         ******      *     *****     *  *********      ***   ***** 
 FINAL  : --------HHHHH-------HHHHHHHHHH---------HHHHHHHHH-------HHHHHHHHHH
 SOL25  : ---B-BBBBBBBBBB-B-B-B-BBB-BB----B-BBB--B--B--BB-B-----B--BB-BB-BB
 SOL5   : ----------BB--B-------BBB--B--------------------------B--BB--B---
 SOL0   : ----------B------------------------------------------------------


 RES    : MPVIAGCREAIKRIAYEFVEMKAKEGVVYVEVRYSPHLLANSKVDPMPWNQTEGDVTPDDVVDLV
 ALIGN  : EEEE---HHHHHHHHHHHHHHHH----EEEEEE--------------------------EEEEEH
 HMM    : HHHHHH-HHHHHHHHHHHHHHHHH---EEEEEEE-----------------------HHHHHHHH
 FREQ   : HHHHH--HHHHHHHHHHHHHHHH---EEEEEEE-------------------------HHHHHHH
 PSSM   : HHHH---HHHHHHHHHHHHHHHHH---EEEEEEE--HH-------------------HHHHHHHH
 CONF   : 88873585789999999999987069639998624331014787777778887777568999999
 NOJURY : ******                 *  *      *  **                   *******  
 FINAL  : HHHHH--HHHHHHHHHHHHHHHH----EEEEEEE-----------------------HHHHHHHH
 SOL25  : B-BBBBB--BBBBBBBBBB---B--BBBBBBBBBBB-BBBB--B--BBB------BBB--BB-BB
 SOL5   : B-BB--B---B--BB--BB-------B--B-B-B--------------------------B--BB
 SOL0   : ----------B--BB---B----------B------------------------------B---B


 RES    : NQGLQEGEQAFGIKVRSILCCMRHQPSWSLEVLELCKKYNQKTVVAMDLAGDETIEGSSLFPGHV
 ALIGN  : HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH----EEEEE--------------HHH
 HMM    : HHHHHHHHHHH----EEEEE------HHHHHHHHHHHHH----EEEEE----------------H
 FREQ   : HHHHHHHHHHHHHHHHEEEEE-------HHHHHHHHHHH---EEEEEE---------------HH
 PSSM   : HHHHHHHHHHH---EEEEEE-------HHHHHHHHHHH-----EEEEE-------------HHHH
 CONF   : 99999975651320256664045787064899999873479935888417888889998862488
 NOJURY :            ***********    **          *   *                  ***  
 FINAL  : HHHHHHHHHHH---EEEEEEE------HHHHHHHHHHHH----EEEEE--------------HHH
 SOL25  : --BB--BB--BBB-BBBBBBBB-----BB--BB-BB--B---BBBBBBBBB---------B--BB
 SOL5   : --BB--B---B---B-BBBBB----------BB-BB-------BBBBBB----------------
 SOL0   : --B---B-------B--B---------------------------B-------------------


 RES    : EAYEGAVKNGIHRTVHAGEVGSPEVVREAVDILKTERVGHGYHTIEDEALYNRLLKENMHFEVCP
 ALIGN  : HHHHHHHH---EEEEE-------HHHHHHHHHHHHHH-----HHH-HHHHHHHHHH----EEEE-
 HMM    : HHHHHHHH---EEEE--------HHHHHHHHHH-----------HHHHHHHHHHHH----EEEE-
 FREQ   : HHHHHHH-----EEE--------HHHHHHHHHH-HHHH------H--HHHHHHHHH---EEEE--
 PSSM   : HHHHHHHH---EEEE--------HHHHHHHHH----------HHHH-HHHHHHHHH----EEEE-
 CONF   : 99998765696488504558882679999986254111012034513899998863488278721
 NOJURY :        *   *   *                ******    ** **            *   *  
 FINAL  : HHHHHHHH---EEEE--------HHHHHHHHHH---------HHHHHHHHHHHHHH----EEEE-
 SOL25  : -BB--B----B-BBBBBBB-B-B-BBB-BB-BB-B-BBBBBB-BB-B--BB-BBB---B-BBBBB
 SOL5   : -BB--B----B--BBBBB-------B--BB--B----B--B--------BB--B------B-BBB
 SOL0   : -----B-------BB-----------------------------------------------B--


 RES    : WSSYLTGAWDPKTTHAVVRFKNDKANYSLNTDDPLIFKSTLDTDYQMTKKDMGFTEEEFKRLNIN
 ALIGN  : -----EEEE-------HHHHH-----EEE-----------HHHHHHHHHH-----HHHHHHHHHH
 HMM    : ------------HHHHHHHHHH----EEE-----------HHHHHHHHHHH----HHHHHHHHHH
 FREQ   : -----EEEEE-------HHHHH----EEE----------HHHHHHHHHHHHH---HHHHHHHHHH
 PSSM   : ----------------HHHHHH----EEE-----------HHHHHHHHHHH----HHHHHHHHHH
 CONF   : 32100200205742416888876994776278866666614789999876616874689999998
 NOJURY :      *****  *****    *                 *          **  
 FINAL  : -------EE-------HHHHHH----EEE----------HHHHHHHHHHHH----HHHHHHHHHH
 SOL25  : BBBBBB-BB--B--BBB--BB---B-BBBBBBB--BB---B--BBBBBB-BB-B---BBB-BBB-
 SOL5   : -B-----B-------BB--B----B-BBBB----------B---B--B----------B--B---
 SOL0   : ---------------------------BB------------------B----------B--B---


 RES    : AAKSSFLPEEEKKELLERLYREYQ
 ALIGN  : HH------HHHHHHHHHHHHH---
 HMM    : HHHH----HHHHHHHHHHHHH---
 FREQ   : HHH-----HHHHHHHHHHHHHH--
 PSSM   : HHH-----HHHHHHHHHHH-----
 CONF   : 756158982889999998476379
 NOJURY :   **               ***  
 FINAL  : HHH-----HHHHHHHHHHHHHH--
 SOL25  : BB-BBBB----B--BB--BB--B-
 SOL5   : -B--B---------B---B-----
 SOL0   : -B----------------------


All done!