make -Wall -Wextra -std 11 -O3 -o multy первый запук multy -i TEST2 fa

$ make
g++ -Wall -Wextra -std=c++11 -O3  *.c++ -o multy

#первый запук

$ ./multy -i TEST2.fas 
Reading sequences...
6 sequences were obtained
Input parameters:
NT substitution matrix  NUC-45
AA substitution matrix  BLOSUM62
Gap open cost           -10
Gap extension cost      -3
Gap frame cost          -15
Stop codon cost         -50

>Gorilla        
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGAGGGACGGC-AGCCTGAACCAGAGCTCTGGGTA
>Otolemur       
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGCGGGACGGC-AGCCTGAACCAGAGCTCCGGGTA
>Equus          
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACAGAGGAGAGGGACGGC-AGCCTGAACCAGAGCTCCGGGTA
>GorillZ
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGAGGGACGGC-AGCCTGAACCAGAGCTCTGGGTA
>Otolemur       
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGCGGGACGGC-AGCCTGAACCAGAGCTCCGGGTA
>Equus          
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACAGAGGAGAGGGACGGC-AGCCTGAACCAGAGCTCCGGGTA

>Gorilla        
MGCVQCKDKEATKLTEERDG!PEPELWV
>Otolemur       
MGCVQCKDKEATKLTEERDG!PEPELRV
>Equus          
MGCVQCKDKEATKLTEERDG!PEPELRV
>GorillZ
MGCVQCKDKEATKLTEERDG!PEPELWV
>Otolemur       
MGCVQCKDKEATKLTEERDG!PEPELRV
>Equus          
MGCVQCKDKEATKLTEERDG!PEPELRV

#второй запуск, больше бонус за неразрывность рамки

$ ./multy -i TEST2.fas -b 10
Reading sequences...
6 sequences were obtained
Input parameters:
NT substitution matrix  NUC-45
AA substitution matrix  BLOSUM62
Gap open cost           -10
Gap extension cost      -3
Gap frame cost          -15
Stop codon cost         -50

>Gorilla        
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGAGGGACGGCAGCCTGAACCAGAGCTCTGGGTA-
>Otolemur       
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGCGGGACGGCAGCCTGAACCAGAGCTCCGGGTA-
>Equus          
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACAGAGGAGAGGGACGGCAGCCTGAACCAGAGCTCCGGGTA-
>GorillZ
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGAGGGACGGCAGCCTGAACCAGAGCTCTGGGTA-
>Otolemur       
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACGGAGGAGCGGGACGGCAGCCTGAACCAGAGCTCCGGGTA-
>Equus          
ATGGGCTGTGTGCAATGTAAGGATAAAGAAGCAACAAAACTGACAGAGGAGAGGGACGGCAGCCTGAACCAGAGCTCCGGGTA-

>Gorilla        
MGCVQCKDKEATKLTEERDGSLNQSSG!
>Otolemur       
MGCVQCKDKEATKLTEERDGSLNQSSG!
>Equus          
MGCVQCKDKEATKLTEERDGSLNQSSG!
>GorillZ
MGCVQCKDKEATKLTEERDGSLNQSSG!
>Otolemur       
MGCVQCKDKEATKLTEERDGSLNQSSG!
>Equus          
MGCVQCKDKEATKLTEERDGSLNQSSG!