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5.0 years ago
amreshsharma.100
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I am reconstructing gene tree using Maximum Likelihood. Multiple Sequences Alignment of Bacterial strains consists of singletons. Should I remove them from alignment then reconstruct phylogeny or should I include them in alignment and then reconstruct tree?
Do you mean "singletons"?
Sorry. Of course its singletons
I'm not sure what you mean by singletons in this context? Can you provide some example data or elaborate your question?
Singletons are sites which contains at least 2 types of nucleotides and occurs multiple times in an alignment.
In the context of multiple sequence alignment and phylogeny reconstruction, singleton are sites at which only one of the species has a distinct nucleotide, whereas all others are the same. For parsimony methods, they are not informative, so sometimes are removed - though it doesn't change the estimated phylogeny, it just saves computation cost. This is not the case for maximum-likelihood (and probably also Bayesian) methods.
Ah, think I’m understanding the question now.
I don’t profess to be an expert but to my knowledge, most ML techniques/tools ignore uninformative sites if necessary, so I don’t see a compelling reason to remove them - you’re just throwing away potentially real evolutionary signal as far as I can work out.
Can you clarify what you mean by that? What exactly are you aligning? Genes, Whole genomes?
I am aligning genes present in different strains of bacteria. After alignment some sites were shown as singletons. I am using Maximum likelihood method for reconstructing tree. Dose these sites affects the phylogeny?