Lineage Separation of Bacterial Sequences
Greetings,
I have a group of sequences from bacterial genome which I want to separate into lineage-sublineage. I have reference genome for the parent lineage and a reference genome for the sublineage. These are separated by differences in SNPs. What good software or code would I use to pull out the lineages from the pool of sequences I have?
Regards.
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For defined genes, MEGA would be an easy option. There are plenty of other programs (phylip, PAUP etc).