MantisBT - MEGA
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0001477MEGA[All Projects] Feedbackpublic2019-10-12 07:582019-10-17 11:24
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gstecher 
normalminorhave not tried
resolvedwon't fix 
MEGA 11 (Graphical Interface version) 
 
Nandita
Mullapudi
mnandita@gmail.com
mnandita@gmail.com
0001477: Long time taken with MEGAX
Dear MEGA team,
Thank you for making such an easy to use tool. I used your program in an in-class bioinformatics exercise where students run MEGAX from their own laptops (varied config). For a data set of 10 viral genomes 0000090:0000030 kb ea (DNA, aligned using CLUSTAL) we found that the alignment was quite slow - and did not finish within the 1.5 hour class period. (On my own laptop at home - an i7 processsor with 16GB RAM it took 30 mins). Would it make a significant difference by using MUSCLE?

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Issue History
2019-10-12 07:58guestNew Issue
2019-10-17 11:24gstecherNote Added: 0004313
2019-10-17 11:24gstecherStatusnew => resolved
2019-10-17 11:24gstecherResolutionopen => won't fix
2019-10-17 11:24gstecherAssigned To => gstecher

Notes
(0004313)
gstecher   
2019-10-17 11:24   
Hi Nandita,

I am writing in response to your question regarding the MEGA software. Yes, for large data, the MUSCLE option for alignment should run significantly faster than the Clustal option. However, the alignment utilities are not designed to work for genome-size data. For very large data sets, you may want to look at using something like MAFFT which is designed for working with larger data.

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