Question: How to convert Multiple sequence alignment format (fasta, Mega etc.,) to binary MSA fasta format for gene gain and loss analysis in GLOOME server?
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gravatar for Dineshkumar K
6 months ago by
Kasaragod, Kerala, India
Dineshkumar K10 wrote:

I need to carryout gene gain and loss analysis of my multiple bacterial genomes in GLOOME server. For which, I need to have binary MSA fasta file and newick format tree. Therefore I need to convert my DNA or Protein MSA fasta format to GLOOME server compatible binary MSA fasta format. I do not know how to convert MSA fasta format to binary MSA fasta format, So please suggest me how do the same. Thank you in advance.

sequence alignment • 408 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Dineshkumar K10

GLOOME server appears to need plain fasta format files. Where are you seeing binary MSA fasta format requirement?

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax70k

This is what GLOOME server required, Required input: The presence and absence matrix. ("1" and "0" or missing data "-")

Sorry, I might have misunderstand with presence and absence matrix and binary matrix. Could you please explain how to make MSA format to presence and absence matrix format.

ADD REPLYlink written 6 months ago by Dineshkumar K10
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