MantisBT - MEGA
View Issue Details
0001932MEGA[All Projects] Feedbackpublic2020-04-20 08:212020-04-23 14:25
guest 
gstecher 
normalminorhave not tried
resolvedno change required 
MEGA 11 (Graphical Interface version) 
 
Stefano
Scilipoti
ss@bios.au.dk
ss@bios.au.dk
0001932: Placement of short reads on constrained topology
I would like to add some short reads without changing the topology of the tree.

Is this possible to do within the MEGA X suite? I know that I could go the RAxML + pplacer way, but I have made the trees with MEGA and it would be more comfortable to keep working with the same software.

Thanks and best wishes,

Stefano
No tags attached.
Issue History
1969-12-31 17:33user19Statusnew => assigned
1969-12-31 17:33user19Assigned To => agasky
2020-04-20 08:21guestNew Issue
2020-04-23 14:25gstecherNote Added: 0004451
2020-04-23 14:25gstecherStatusnew => resolved
2020-04-23 14:25gstecherResolutionopen => no change required
2020-04-23 14:25gstecherAssigned To => gstecher

Notes
(0004451)
gstecher   
2020-04-23 14:25   
Hi Stefano,

I am writing in response to your question regarding the MEGA software. I am not sure I understand what you are trying to do but it sounds like you might want to try the user tree analysis in MEGA. If you already have a tree in a newick file then from the main form you can run User Tree->Analyze User Tree by Maximum Likelihood where your two input data files will be the newick file and a multiple sequence alignment that has the short reads added. I am not sure if this is what you really want but it sounds like the closest thing available in MEGA.

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu