Procedure

1.    Follow (http://vlab.amrita.edu/index.php?sub=3&brch=311&sim=1835&cnt=2) to install R in personal computer.
2.    Install the SeqinR package.
                   Import “seqinr” library to R workspace
                    Create a function() for retrieving multiple sequence from database

    Function 1
        create a list to store sequences
        connect to the database
        for each element in the array
            query the sequence and assign to a variable 
            append the data into a list
        end
        close the connection
        return list
    end of fuction 1
                    Create a vector of sequences
                   Retrieve the sequences from the database
                    Write the sequences into a file
                    Align the sequence and assign to a variable in phylip format

Procedure to work Simulator

• Consider three random protein sequences: Protein Sequence 1, Protein Sequence 2, Protein Sequence 3. 

.fasta format aminoacid sequences were aligned using multiple sequence alignment with sequinR package. The dist.alignment() function takes a multiple alignment as input and calculates calculates the genetic distance between each pair of proteins in the multiple alignment.

• Click on run button to execute simulator. 

The numerical values in matrix of the output indicates genetic distance between each pair of proteins in the multiple alignment. The larger the genetic distance between two sequences, the more amino acid changes or indels that have occurred since they shared a common ancestor, and the longer ago their common ancestor probably lived.