Can I make a phylogenetic tree from multiple plant biological name within the family, or, from distant family?
Thanks in advance.
Thanks a lot Qi Guo.
In case, I only have the biological name of the plants, the sequence data is not available or the plants are not well sequenced, is there a way to build phylogenetic tree using only those biological names?
Thanks again.
Inferring phylogenetic trees depends on nucleotide sequences. When the sequence fragments are partially missing, MEGA's "Align" function is good at aligning the valid parts to build the phylogenetic tree. However, I don't quite understand what you mean by constructing a phylogenetic tree using only biological names. If I guess correctly, are you trying to say that the outgroups of the phylogenetic tree are constructed by relying only on the biological names without any sequences? It seems to me that this can't be done in MEGA, first of all the phylogenetic tree needs to be constructed based on the differences or affinities of the sequence fragments, and this obviously won't work if there is no information about the sequences. However, you can "artificially" add outgroups by manually modifying the tree file, but the root of the tree, must be considered before adding outgroups. If this is not taken into account, then the tree is probably incorrect. In addition, when you choose to add outgroups manually, rather than relying on a program to calculate them, you may need to ignore the branch lengths, since it is obviously impossible to know the length of the outgroups in the tree in this situation. Overall, adding outgroups manually is not recommended.
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