Procedure for phylogenetic analysis :
Go to simulator tab to know more about how to retrieve the query sequence .
Procedure For PHYLIP :
Align the multiple DNA sequences (output of the ClustalW) and save it in PHYLIP format as infile.phy. Start the program of Dnadist by clicking the icon and giving this infile as input.
All the PHYLIP programs are menu driven programs. Dnadist will calculate pairwise distances between the sequences. At first, Dnadist will ask whether the input file is there in the PHYLIP folder. If the file does not exist, it will ask you to give the correct file name. After giving the correct input, if needed it will ask to change any settings for the program by typing the first letter or number. If the changes are not required, by typing ‘Y’ it will start running the program. Output will return to the file as outfile, so that the output of this file can be used as input of another program. Output would be as represented in Figure 1.
Figure 1: Distance Representation
Like Dnadist, Neighbor also gives sequence distance analysis. Output of Dnadist is given as input to Neighbor. Output file and tree file will be returned to outfile and outtree as represented in Figure 2 .
Figure 2 : Sequence distance analysis.
Branch lengths and tree are represented with the help of Neighbor joining method. The outfile and outree after the Neighbor joining method are given below (Figures 3 & 4).
Figure 3: Outfile
Figure 4: Outtree
Cladogram is represented via Consensus tree program. Input for the cladogram will be output (outtree) of Neighbor program which will generate outfile and outtree. It represents the consensus tree. Numbers on the branches indicate the number of times the species has been partitioned into two sets separated by that branch occurred among the trees. Here the outfile and outtree are represented in Figure 5 and Figure 6.
Figure 5 : Cladogram representation (outfile).
Figure 6 :Cladogram Representation (outtree).