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Wardah Abd Rahman
Siputeh, Perak.
Soalan pertama saya : What is the difference between original tree and bootstrap consensus tree in MEGA?
After constructing a phylogenetic tree using MEGA 4, i noticed that there were 2 tabs at the upper of the tree window. On the left is original tree and next to it, is bootstrap consensus tree. Both did show the picture of the tree. Which one should i take as the result?
Jawapan oleh penyumbang utama-BioLiz:
Jawapan oleh penyumbang utama-BioLiz:
A bootstrapped version is always better, since it will show the "robustness" of the tree. The bootstrapped version should show numbers at each branch of the tree, but otherwise the tree will look the same. These numbers are actually percentages - how many times these branches were still together in a randomized re-do of the tree. The higher the number, the more confident you can be that the subbranches on that branch have a common ancestor. But numbers lower than 50% are usually not displayed.
Source(s):
Soalan kedua saya : How to do sub-clustering from phylogenetic tree?
I'm constructing a phylogenetic tree from a total of 70 DNA sequences. These isolates consisted of 6 different species with the same genus (species A=14 isolates, species B=10 isolates....total=70). The problem is the result tree had many branches that makes me confuse on how to sub clustering it. Is there any guideline that i can used? Please, help me solve this problem..
Additional Details
Firstly, thanks BioLiz for answering 3 of my questions =)
The link is helpful and your explanation did give me a new information on how to display the sequences.
Back to the 'sub-clustering', i think the term that i used was wrong. Actually, i tried to refer to the clusters or should i call it clades? I noticed that in certain publication, they did some kind of 'clustered' their isolates. What i'm trying to say is, from a phylogenetic tree, we can directly see the major branch formed e.g. two clusters (I and II). Then, from these main clusters, many more branches come out and form a few sub-clusters. Is there a way or guideline on how to grouped the isolates in these sub-clusters? They used liked sub-clusters A, B, C etc. to explain the close related species, the same-shared bootstrap value etc.
Jawapan oleh penyumbang utama-BioLiz:
I am not sure what you mean by "sub clustering", and I am not familiar with MEGA (which is what you probably are using, based on the previous question that I answered). Assuming you want to find a way of highlighting the isolates from 1 species, I would work with colors. Give each species a different color, but I am not sure if you can do that in MEGA.
You could also export the tree picture, e.g. as a .ps file (if possible) and change the colors of the endpoint species in Adobe Illustrator.
Or, you could export the tree out of MEGA as a Newick file, and color it in e.g. Dendroscope.
http://www-ab.informatik.uni-tuebingen.d…
I hope this is a bit helpful. Again, I am not sure if this is what you asked, but I am working on phylogenetic trees containing thousands of sequences, so I am always looking for creative ways to display them. Here is a tree made with hundreds of rDNA sequences, in which species names was given a different color according to their phylum. You cannot read the species names, but the colors are easy to see. Sorry for the small picture, I cannot give you the full picture, unless you have a subscription to Science magazine.
Good luck!
Soalan ketiga saya : Is forward and reverse primers amplified too during PCR?
The link is helpful and your explanation did give me a new information on how to display the sequences.
Back to the 'sub-clustering', i think the term that i used was wrong. Actually, i tried to refer to the clusters or should i call it clades? I noticed that in certain publication, they did some kind of 'clustered' their isolates. What i'm trying to say is, from a phylogenetic tree, we can directly see the major branch formed e.g. two clusters (I and II). Then, from these main clusters, many more branches come out and form a few sub-clusters. Is there a way or guideline on how to grouped the isolates in these sub-clusters? They used liked sub-clusters A, B, C etc. to explain the close related species, the same-shared bootstrap value etc.
Jawapan oleh penyumbang utama-BioLiz:
I am not sure what you mean by "sub clustering", and I am not familiar with MEGA (which is what you probably are using, based on the previous question that I answered). Assuming you want to find a way of highlighting the isolates from 1 species, I would work with colors. Give each species a different color, but I am not sure if you can do that in MEGA.
You could also export the tree picture, e.g. as a .ps file (if possible) and change the colors of the endpoint species in Adobe Illustrator.
Or, you could export the tree out of MEGA as a Newick file, and color it in e.g. Dendroscope.
http://www-ab.informatik.uni-tuebingen.d…
I hope this is a bit helpful. Again, I am not sure if this is what you asked, but I am working on phylogenetic trees containing thousands of sequences, so I am always looking for creative ways to display them. Here is a tree made with hundreds of rDNA sequences, in which species names was given a different color according to their phylum. You cannot read the species names, but the colors are easy to see. Sorry for the small picture, I cannot give you the full picture, unless you have a subscription to Science magazine.
Good luck!
Soalan ketiga saya : Is forward and reverse primers amplified too during PCR?
Some of my isolates have the same sequence as the forward primer in the beginning of the sequence. Is the primers amplified too during PCR that subsequently it can be noticed during the DNA sequencing of the isolates? If i want to proceed with constructing a phylogenetic tree, is it true that the sequence data only valid if i cut off/delete the look-alike primer sequence?
Thank you in advance!
Jawapan oleh penyumbang utama-BioLiz:
Yes, primers are amplified too. In fact, most of your sequences from your PCR product will have the exact sequence as the primer sequence in that region, but the primers you offer during PCR will be used to make the new strand. So you can never be 100% sure what the original sequence in that region was.
In scientific publications, we usually do not use these primer regions. We will use a filter that will ignore them, when we build a phylogenetic tree, and we will remove them (by using a filter) when we submit them for publication. Well, most scientists should do that.... not all of them do that unfortunately.
But you can leave them in, in your alignment. I like to give my F and R primer a different color, so I can see when I reached the end of my alignment.
Thank you in advance!
Jawapan oleh penyumbang utama-BioLiz:
Yes, primers are amplified too. In fact, most of your sequences from your PCR product will have the exact sequence as the primer sequence in that region, but the primers you offer during PCR will be used to make the new strand. So you can never be 100% sure what the original sequence in that region was.
In scientific publications, we usually do not use these primer regions. We will use a filter that will ignore them, when we build a phylogenetic tree, and we will remove them (by using a filter) when we submit them for publication. Well, most scientists should do that.... not all of them do that unfortunately.
But you can leave them in, in your alignment. I like to give my F and R primer a different color, so I can see when I reached the end of my alignment.
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