. .
Phylogenetic Analysis using PHYLIP - Rooted trees



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


Rooted trees are represented via Drawgram by providing the input as the "outfile" obtaining from neighbor joining method. Rooted tree considers an imaginary root as the start and from that the other sequences are aligned.



Figure 5: Rooted tree







Cite this Simulator:

..... .....

Copyright @ 2022 Under the NME ICT initiative of MHRD

 Powered by AmritaVirtual Lab Collaborative Platform [ Ver 00.13. ]