How to draw phylogeny tree for long genomes? ('msa' taking much time)
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 17 months ago
India

How to draw phylogeny tree of 1100 genomes belonging to diffrent linages of same spices, Where each sequence consists of ~100000 SNPs locations of genome, I tried 'msa' package with default parameters, but it is taking much longer time. Please suggest me any trick to do this.

msa phylogenetic • 673 views
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UBodenhofer ▴ 290
@ubodenhofer-5425
Last seen 12 weeks ago
University of Applied Sciences Upper Au…

I do not understand why you use 'msa' for that purpose. If you are considering SNP data, the SNPs are already aligned, so there is no need to align the genomes. I also wonder how you can deal with SNPs across different species. Please specify in much more detail what your setup is and what you want to do.

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