To construct a phylogenetic tree using data from different regions of the 16S gene, is it necessary to insert the short sequences into the full-length sequences before constructing the tree? If so, what is the current method usually used? Looking forward to your kind responses! Thanks a lot!
Use MEGA software for construction of phylogenetic tree (NJ and ML) and tree contraction needs full length of genes.
Mansoor Khan, thank you very much for the kindly and professional answer, I will try the methods
Daniel Carrera Lopez
, thanks very much for your friendly and detailed advice, I will try the methods you mentioned right away, thanks!
If you would construct a full-length 16S tree, you need to align the sequences and make the sequence length as same as possible to reduce the missing data and improve the support value. NJ and ML tree are common for 16S.
RAxML and IQtree are good for inferring ML tree, and FigTree for visualization.
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