0001429: error if number of sequence is too large - MantisBT

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ID

Project

Category

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Date Submitted

Last Update

0001429

MEGA

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public

2019-09-20 09:15

2019-09-20 14:13

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

not fixable

Platform

OS

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0001429: error if number of sequence is too large

Description

Hi,

I am trying to codon align 13000 sequences using muscle but it always gives me an error. It works fine when I tested mega with about 3000 sequences. I could probably just use the muscle software but it won't allow me to do codon alignment not like in mega.

I was wondering if there is any fix to this.

Julius

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First Name

Julius

Last Name

Campecino

Email

campecin@msu.edu

Confirm Email

campecin@msu.edu

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Notes
(0004305) gstecher (administrator) 2019-09-20 14:13	Hi Julius, I am writing in response to your question regarding the MEGA software. For aligning that many sequences I think your best option is to use an alignment program that is designed to handle larger numbers of sequences such as MAFFT. Unfortunately, MEGA does not handle that much data very well for sequence alignment. You might also be able to do something like: translate codons to amino acids align amino acids map the aligned amino acids back to original codon data using something like http://wbiomed.curtin.edu.au/bioinf/CodonAlign.php [^] or a custom script -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
2019-09-20 09:15	guest	New Issue
2019-09-20 13:57	gstecher	Note Deleted: 0001218
2019-09-20 13:57	gstecher	Note Deleted: 0001222
2019-09-20 13:57	gstecher	Note Deleted: 0001251
2019-09-20 13:58	gstecher	Note Deleted: 0001250
2019-09-20 13:58	gstecher	Note Deleted: 0001249
2019-09-20 13:58	gstecher	Note Deleted: 0001223
2019-09-20 14:13	gstecher	Note Added: 0004305
2019-09-20 14:13	gstecher	Status	new => resolved
2019-09-20 14:13	gstecher	Resolution	open => not fixable
2019-09-20 14:13	gstecher	Assigned To	=> gstecher

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