### RKalign
##  Effective alignment of RNA pseudoknot structures 
using partition function posterior log-odds scores 

##  This package contains the executable RKalign.jar file.
##  To run the program, Java SE Development Kit 7u51 
(jdk-7u51) or a later version must already be installed on
your computer. If not, please first download it from 
the ORACLE website.

### Required external data:
##  Scoring matrix file: RIBOSUM85_60 file
##  Input file:
#   (1) For pairwise alignment, use the sample input file P_Sample_Input.txt.
#   (2) For multiple alignment, use the sample input file M_Sample_Input.txt.
##  Notes on data:
#   In case your data contains recursive or nested pseudoknots, 
the following characters can be used to represent 
the base pairs in these pseudoknots: 
"()", "[]", "{}", and from "Aa" to "Zz".

### Run the RKalign program:
##  Put all the files in the RKalign.zip package 
in a folder named RKalign.
##  Usage:
    java -jar RKalign.jar [OPTION] INPUT.txt
##  Description:
#   Align the RNA pseudoknot structures in the INPUT.txt file.
#   Options:
    -p:  for pairwise alignment
    example:  java -jar RKalign.jar -p P_Sample_Input.txt
    -m:  for multiple alignment
    example:  java -jar RKalign.jar -m M_Sample_Input.txt
#   The program automatically writes the output into a file named OUTPUT.txt.

### Output file description:
##  P_Sample_Output.txt is a sample output file for pairwise alignment.
##  M_Sample_Output.txt is a sample output file for multiple alignment.