1 / 15

How to generate phylogenetic tree using the CART function

Programs needed. You need program(s) to generate multiple sequence alignment and phylogenetic trees.We recommend the MEGA program, which can be freely obtainable athttp://www.megasoftware.net/. Identifying a strain. We will use a Genbank entry (EF379568) as an example. Let's assume that this is yo

marrim
Télécharger la présentation

How to generate phylogenetic tree using the CART function

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

    1. How to generate phylogenetic tree using the CART function

    2. Programs needed You need program(s) to generate multiple sequence alignment and phylogenetic trees. We recommend the MEGA program, which can be freely obtainable at http://www.megasoftware.net/

    3. Identifying a strain We will use a Genbank entry (EF379568) as an example. Lets assume that this is your own sequence.

    5. Identify Paste your own sequence in Identify page

    6. You should be re-directed to the Results page. To add your query sequence to the cart, click [Add query to cart] button. You will be re-directed to the Cart page.

    7. Now your cart has your query sequence. Go to the Results page to view the identification results again

    8. Now, click [Add to cart] button. This will add all phylogenetic neighbors to the cart. You will be re-directed to the Cart page.

    9. Now, your cart contains sequences of your query and phylogenetic neighbors.

    10. In addition, you can add sequences of a genus of your choice into the cart. Click the green button to add all species in the genus Marinobacterium (arrow below). You can add species in the other genera by clicking green buttons.

    11. Download sequence file (fasta format), and save it on your local hard disk. I will name our file test.fasta.

    12. Open sample.fasta with MEGA program. Align sequences by choosing Alignment/Align by ClustalW. Note that the EzTaxon entries are labeled (flanked) with zZ.

    13. After multiple alignment, YOU NEED TO TRIM ambiguously aligned positions. Select region (to be deleted) while holding left mouse button pressed. Then, choose Edit/Delete to delete selected region. Generally, trim both ends and internal regions, if necessary.

    14. Save trimmed alignment as sample_align.meg. Generate phylogenetic trees as you wish. MEGA offers the following treeing algorisms. Neighbor-joining Minimum evolution Maximum parsimony Bootstrap analysis (1,000 times recommended) A neighbor-joining tree with 1,000 bootstrap analysis is given at the left side. This tree is labeled with zZ flanked accession numbers by EzTaxon server. You can change the labels using various formats. To do this, first save the tree as a newick file. Choose File/Export Current Tree(Newick) in MEGA treeview mode. Save/export your tree as sample.nwk. Go back to EzTaxon server.

    15. To change labels in tree or any other text files, choose Replace accession. Then, select a format of your choice. We will select IJSEM format to convert sample.nwk file. Save converted file as sample.tre and open it using MEGA or other tree viewing programs.

More Related