Dear all,
I have some bacteria DNA partial sequences (16s rRNA). They sequenced only by 9 F primer. Their length is under 1100 bp. When I draw phylogenetic trees for some of them by MEGA, my sequences pleced in separate branches. So, how can I identify my sequences in this case, because they are not in a sister group.
Thank you
I suggest you use BLAST at NCBI and download the sequences from the Type strains closest to your sequences. Then use MEGA software do a multiple alignment of your and the downloaded sequences and draw a phylogenetic tree. That tree will give you a reeliable answer to base identification. NCBI BLAST has a tree drawing function that will automatically draw a tree for you. Which would give you an immediate answer. Best wishes and keep up the good work.
I suggest you use BLAST at NCBI and download the sequences from the Type strains closest to your sequences. Then use MEGA software do a multiple alignment of your and the downloaded sequences and draw a phylogenetic tree. That tree will give you a reeliable answer to base identification. NCBI BLAST has a tree drawing function that will automatically draw a tree for you. Which would give you an immediate answer. Best wishes and keep up the good work.
Incomplete sequences will be place on separate branches because the trees are probably using a likelihood approach for assignment. What it is saying is that, based on the complete dataset, there's a reasonable probability that these sequences differ from the others.
@Mark Farman
Dear Professor Farman,
Thank you very much for your guidance.
Note that I have seen the same behavior with sequences that only differ by indels, despite the fact that indel positions are not considered by the program I am using: RAxML.
Mark Farman Sir I have also an issue, I have read all answers here, I have 10 fungal isolate sequences, ITS, the genera is same however species may be different, how will I make a phlogenetic tree? Will I search each separatly in NCBI and download sequences and then combine all or there is an another easy method Thanks
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