hello,
The sequencing of the 16S DNA of two strains showed after introduction of their sequence on NCBI by comparing them with the sequences of the authors that belong to the genus Pseudomonas aerginsa and Bacillus aquimaris. I want to choose an out group to build my phylogenetic tree. How can I choose it in this case? It can be what for example?
Starting with a set of summary records in the Taxonomy database...
Choose Taxonomy Links from the Display pull down list at the top of the results.
Choose "Common Tree" from the Display pull down menu.
The page will re-load with a Common Tree display. The Common Tree display shows a hierarchical view of the relationships among the taxa and their lineages. Individual nodes in the tree link to the Taxonomy Browser. Controls on the Common Tree allow expanding / collapsing nodes, choosing a subset to redisplay, deleting taxa, adding taxa, and saving the tree in several formats.
https://www.ncbi.nlm.nih.gov/guide/taxonomy/
you can build an un-rooted tree without an out-group, if you want to root the tree you can choose any E-coli strain as an outgroup in this case
thank you Mr Ifran Hussain, But on what basis you have chosen E.coli like an out-group?
In general, an outgroup should be as close as possible to the ingroup. If there is a risk that it is really part of the ingroup, then other outgroups are needed in addition, to help resolve those relationships. Multiple outgroups give a more reliable picture.
For example, if you're trying to compare your species with other gram-positve species, and trying to highlight similarities in Gram-positive species compared to gram-negative. Or highlight differences between gram-positive to gram negative. Then using a gram-negative bacteria makes sense.
if you're trying to show how unique or different your bacteria is, then it would make more sense to compare it to other close species that are gram-positive.
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