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?
gravatar for Dineshkumar K
18 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 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 • 1000 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by Dineshkumar K40

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

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax85k

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 18 months ago by Dineshkumar K40
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