I want to construct a phylogenetic tree of bacteria genus. I downloaded data from NCBI and then extracted 16s genes with Barrnap. Then I aligned 16S rRNA sequences using MAFFT. But the number of sequences is bigger than the number of strains I had initially. i have 689 sequences for 113 strains. I do not know what to do now to proceed with building tree. I did trimming and removed sequences that had a lot of gaps what do I do now? Do I need to aligh the sequences with the shared ID's ? for example : >CP156916.1:38877-40386 +
>CP156916.1:41004-43835 . They have the same ID but different ranges
It is always best if you use the identical region from each species in the alignment. Ideally it would use the full 16S gene and they would be almost identical in length. Because each species has multiple copies of the 16S gene, you can get different genomic regions. They should be identical or almost identical in sequence. Thus, if you aligned them you in a tree you should get a very tight cluster for each read from the same species and the tree structure would come from the different species. Alternatively, try building a consensus or just alignment from a single species to check that they are almost identical.
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