I am trying to build the phylogenic tree using PhyML in Genious Prime and its offers me the Substutin model for which I used TN93, branch support bootstrap and for the optimize it has several options Topology/length/rate, Topology/length, length/rate, length, rate or none and I don't what they are and how it will affect my results. Can anyone help me to understand this.
In the area of artificial intelligence or machine learning, unfortunately there does not exists a unified approach/method/technique/algorithm/model which may produce optimal outputs for every given database (or domain). The best way is however., model selection, i.e., to choose some particular appropriate according to mood/nature/quality of the given database. Also some data preprocessing may enhance accuracy a bit more further.
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