Phylogenetic trees  (Page 3/3)

Look at the multiple sequence alignment scoring section. Notice the sequence list that assigns numbers to each sequence. The alignment scores are labeled by the assigned sequence numbers, so this list is necessary to interpret the scores.

Return to the top of the page and select "Import Alignment(s)". This will save this sequence alignment under the "Alignment Tools" menu of this session. Select the alignment by clicking in the small box to the left of the listing. Choose "DRAWGRAM" from the options box, to view this alignment in a rooted tree. Accept all the default values on the drawgram page and click the submit button at the bottom of the page. Drawgram will return a rooted tree using the program "PHYLIP" , a Phylogeny Inference Package. The PHYLIP suite includes packages that can infer phylogenies by parsimony, compatibility, distance matrix methods, and maximum likelihood methods. PHYLIP can also draw several types of tree diagrams, and allows editing of trees. The suite accepts an impressive number of input formats, including nucleotide and protein sequences in fastA format. Detailed information on the PHYLIP suite can be viewed at the PHYLIP website .

Click on the "Return" button and this will yield the "Alignment Tools" menu. It will be necessary to return to "Protein Tools" to complete this tutorial, so select the "Protein Tools" icon with the mouse.Now, to put together a little more complex cladogram, search the PDBFINDER in the Ndjinn Database for the following sequences by copying and pasting the following into the query box:

Import all of these sequences into this session.Once again, there are some duplicated sequences from multimeric proteins, so delete 2AAC_B, 1KAN_B, 1AUX_B and 1DUB_B, C, D, E, and F. This shouldleave 11 sequences, including the first four sequences imported in the example above. On the scroll down menu under "Protein Tools", highlight"Select all sequences" and click "Run". Next, select "ClustalW" and click "Run". On the ClustalW input page, change the "unrooted" tree option to"rooted and unrooted trees", then submit.

Attempt to construct another type of tree using sequences of personal interest, without explicit instructions.