How to convert Multiple sequence alignment format (fasta, Mega etc.,) to binary MSA fasta format for gene gain and loss analysis in GLOOME server?

Question

[Kumar]

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.

[GenoMax]

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

[Kumar]

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.