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Old 07-31-2013, 04:19 AM   #1
juannajuann
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Question phylogenetic tree construction

Hi,

I have isolated

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Old 07-31-2013, 04:32 AM   #2
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Hi,

I have isolated 9 soil bacteria and sent for sequencing. I had identified them using BLASTn. The results showed that 5 of them belong to genus Bacillus, 2 strains belong to genus Serratia , 1 strain is genus Pseudomonas and 1 strain belong to genus Escherichia.

Now, I would like to construct phylogenetic tree. However, I not sure how to do it.
So, can I just construct a phylogenetic tree that only consists 9 strains of my study bacteria samples?
Or do I need to construct a phylogenetic tree that consists of my study isolated bacteria together with some related bacteria species??

Please help me to remove all my doubt... Thanks.
Basically, you can construct a phylogenetic tree from any set of related sequences. However, to construct a robust tree, you need to have all the relevant taxa well (evenly) represented, as well as a well thought-out outgroup. Maybe your best bet would be to simply take 16S/other marker genes and add it/them to some pre-made alignment/s?

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Old 07-31-2013, 04:57 AM   #3
juannajuann
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Basically, you can construct a phylogenetic tree from any set of related sequences. However, to construct a robust tree, you need to have all the relevant taxa well (evenly) represented, as well as a well thought-out outgroup. Maybe your best bet would be to simply take 16S/other marker genes and add it/them to some pre-made alignment/s?

So, you mean the phylogentic tree include my bacteria strain and some related species...
It is the phylogenetic somehow look like this, just for example

[IMG][/IMG]

Sorry, I am new in this thing. So, I am not sure how to do it.
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Old 07-31-2013, 05:08 AM   #4
rhinoceros
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So, you mean the phylogentic tree include my bacteria strain and some related species...
What is the question you want to answer with your tree? If it's the taxonomic placement of your samples, then obviously constructing a tree that includes only your samples will not take you very far. For precise taxonomic placement, you really should just add your sequences to some pre-made alignment..
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Old 07-31-2013, 05:28 AM   #5
juannajuann
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There is some journal that construct phylogenetic tree using the isolated strains only...
for example,



............Well, basically I just want to study the evolutionary relationship among the isolated bacteria. I just not very sure the best way to construct the phylogenetic tree.
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Old 07-31-2013, 07:41 AM   #6
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You can use just your isolated samples if you are only interested in the relationships amongst them. If you wish to generate a rooted tree, then you will need an appropriate outgroup (preferable several sequences, not just one arbitrary one).

But you can generate unrooted cladograms with the sequences you have.

A free suite of tools like PHYLIP will let you explore using distance, ML and Parsimony methods. There are other free tools to explore Bayesian methods or alternate models as well.

Be wary of misinterpreting branch lengths though, if you are not able to flesh out the data set with additional related species.
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