0001477: Long time taken with MEGAX

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0001477

MEGA

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2019-10-12 07:58

2019-10-17 11:24

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

won't fix

Platform

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0001477: Long time taken with MEGAX

Description

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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First Name

Nandita

Last Name

Mullapudi

mnandita@gmail.com

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mnandita@gmail.com

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Notes
(0004313) gstecher (administrator) 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

Issue History
Date Modified	Username	Field	Change
2019-10-12 07:58	guest	New Issue
2019-10-17 11:24	gstecher	Note Added: 0004313
2019-10-17 11:24	gstecher	Status	new => resolved
2019-10-17 11:24	gstecher	Resolution	open => won't fix
2019-10-17 11:24	gstecher	Assigned To	=> gstecher