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(0003367)
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user614
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1969-12-31 17:33
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Hi Meghyn,
I am writing in response to your question regarding parsimony tree construction using the MEGA software. I think the two trees you are getting are actually the same but are just arranged differently. To see this, try using the Subtree->Root tool to place the root on the same branch in each tree. You might also need to click on View->Arrange Taxa->By input order. Please let me know if this does not help.
Best regards,
Glen Stecher |
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(0003369)
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user614
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1969-12-31 17:33
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Hi Glen,
Yes, that is what I am doing. Thank you. I just wanted to know, because I have to add my research sequences to the tree and will have to regenerate the results myself.
I may enlist your help again in the future if it is not too much trouble.
Thanks again,
Meghyn
From: Glen Stecher [mailto:gstecher@mainex1.asu.edu]
Sent: Thursday, March 13, 2014 12:15 PM
To: Meghyn Meeks
Subject: RE: MEGA question
Hi Meghyn,
I used MUSCLE with the default settings but the file I sent you is already aligned so you can just run the analyses directly with that file. In that way you can guarantee that both versions are using the same alignment.
Best regards,
Glen Stecher
Application Programmer
Center for Evolutionary Medicine
Phone: 480-965-3880
Web: http://cemi.asu.edu [^]
From: Meghyn Meeks [mailto:Meghyn.Meeks@tamu.edu]
Sent: Thursday, March 13, 2014 10:13 AM
To: Glen Stecher
Subject: RE: MEGA question
Hi Glen,
Thank you for helping me. I am regenerating a tree based on the alignment you sent me. Can you please specify which method you used, either ClustalW or MUSCLE?
Thanks,
Meghyn
From: Glen Stecher [mailto:gstecher@mainex1.asu.edu]
Sent: Thursday, March 13, 2014 12:01 PM
To: Meghyn Meeks
Subject: RE: MEGA question
Hi Meghyn,
I replicated the analysis and I see very little difference between the results from MEGA5 and MEGA6. In the bootstrap consensus trees confidence values are very low in cluster A (but the topology is still quite similar) and if I compute a condensed tree, the results are identical between versions. I think the difference you get must arise from the alignments used. The captions in the tree session files you sent me show different number of sites (804 in one and 816 in the other) used between results so perhaps the settings used for alignment were different between analyses or the data used was not exactly the same. Attached is the alignment I used for both versions to replicate the analysis.
Best regards,
Glen Stecher
Application Programmer
Center for Evolutionary Medicine
Web: http://cemi.asu.edu [^]
From: Meghyn Meeks [mailto:Meghyn.Meeks@tamu.edu]
Sent: Thursday, March 13, 2014 8:57 AM
To: Glen Stecher
Subject: RE: MEGA question
Yes, thank you.
From: Glen Stecher [mailto:gstecher@mainex1.asu.edu]
Sent: Thursday, March 13, 2014 10:54 AM
To: Meghyn Meeks
Subject: RE: MEGA question
Hi Meghyn,
Could you send me the alignment file that was used so that I can replicate the analysis? The results done in MEGA5 only has a consensus tree (made from 5 equally parsimonious trees) but the results done in MEGA6 has 7 equally parsimonious trees. The difference may arise from treatment of ambiguous data but I will need to replicate the analysis to understand the difference. Of course your data would be kept confidential.
Best regards,
Glen Stecher
Application Programmer
Center for Evolutionary Medicine
Web: http://cemi.asu.edu [^]
From: Meghyn Meeks [mailto:Meghyn.Meeks@tamu.edu]
Sent: Thursday, March 13, 2014 8:26 AM
To: Glen Stecher
Subject: RE: MEGA question
Hi Glen,
Thank you for your quick response.
Please see the bootstrap consensus tress in the attached figures. I believe I have already done what you suggested. My problem are with sequences that are in CLUSTER "A."
Any ideas? I did not change the sequences in any manner. I just aligned with MUSCLE and clicked DATA >PHYLO ANALYSIS > MP Tree.
Thank you,
Meghyn
From: Glen Stecher [mailto:gstecher@mainex1.asu.edu]
Sent: Thursday, March 13, 2014 10:19 AM
To: Meghyn Meeks
Subject: MEGA question
Hi Meghyn,
I am writing in response to your question regarding parsimony tree construction using the MEGA software. I think the two trees you are getting are actually the same but are just arranged differently. To see this, try using the Subtree->Root tool to place the root on the same branch in each tree. You might also need to click on View->Arrange Taxa->By input order. Please let me know if this does not help.
Best regards,
Glen Stecher
Application Programmer
Center for Evolutionary Medicine
Web: http://cemi.asu.edu [^] |
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