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Firstly its good you've done some proofing of your output wherein you spotted, 75000 The alignment output is approximately double the genome size, just over double the input. An off-question point, I assume the computer you are working on has at least 8-cores because thats what you are requesting. Clustal omega is a very solid algorhithm and has been ...


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Have you had a look at your alignment? I personally use Jalview but any alignment viewer should work. Colour > Percentage Identity (or Nucleotide) should help with visualization. Does the alignment look reasonable (and gaps are just inserted at the end for some reason), or is it pretty messy? If it looks messy, is it just a few outlier sequences that ...


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You might have some luck with Parsnp. From the description: Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual ...


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That's a LOT of sequences! I'm doubtful you'd be able to get TripletRes or CCMPred to run at all with an MSA depth of 1.5 million. I suggest pruning your dataset to remove redundant sequences (sequences which don't add much information, i.e. the ones which differ only 1 or 2 AA). I'm curious if your Neff (normalized number of effective sequences--as defined ...


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