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Hi Margaret,
I am writing in response to the bug report you recently submitted regarding the MEGA software. A description of the MEGA sequence alignment format is given in the help documentation at Part III: Input Data Types and File Format -> MEGA Input Data Formats. Additionally, there are example files included in MEGA that you can open in a text editor (the files are in Documents\MEGA7\Examples). If that does not help, you can always just put your data in a FASTA formatted text file and use that.
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Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu |
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Hi Margaret,
Most of the analyses in MEGA for sequence data require that the sequences are aligned, so when you open a MEGA formatted file, if any sequences are of unequal length, MEGA will complain. If the sequence data is already aligned, you should be able to add indel characters to the end of all sequences that are shorter than the longest one. If the data is not yet aligned, you should put the data in a FASTA formatted file, open that file in Alignment Explorer, perform sequence alignment, then export the data to either FASTA or MEGA format.
On 5/12/2017 12:01 PM, Davis, Margaret wrote:
> Thanks for your response! That helps a lot. I was able to get the file into the correct format to be accepted by the Alignment window.
> One thing that confuses me is that when I get the Mega format into the Alignment window, it tells me the sequences have to be the same length. Yet the examples have sequences that are not the same length. I don't like trimming sequence arbitrarily to the same length. Do you have any advice?
>
> Thanks again,
> Margaret |
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