Phylogenetic Analysis

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Questions related to Phylogenetic Analysis

Why does MrBayes translate my taxa labels?

Hi all, I'm running the new version of MrBayes and I'm using Mega to look at the resulting tree. I noticed that MrBayes automatically includes a translate block in the tre file, substituting the...

27 June 2016 7,587 2 View

Anyone know of an algorithm to programmatically rearrange a phylogenetic tree upon rooting on a given branch?

Our program already produces a tree. We would like to allow the user the choice to root the tree on an external or internal branch, but the resulting change in the tree needs to be coded - and we...

13 June 2016 1,393 13 View

Will the topology of a phylogenetic tree change after removing a number of sequences and re-run the treeing method?

Hello, suppose I have constructed a phylogenetic tree with all OTU sequences and reference sequences. I now want to have a tree containing only the OTU sequences. Is it a good practical to remove...

11 June 2016 8,444 4 View

If I have low bootstrap values in a ML tree, does it mean that there is no separation between different genera?

I have a maximum likelihood tree (18S and COI) for a nematode family which contains 4 different genera. The bootstrap values were very low and all the 4 genera are intermingled in both trees with...

06 June 2016 6,096 6 View

Why does MrBayes translate my taxa labels?

Hi all, I'm running the new version of MrBayes and I'm using Mega to look at the resulting tree. I noticed that MrBayes automatically includes a translate block in the tre file, substituting the...

06 June 2016 3,002 2 View

What are the mathematical approaches to prove that a DNA sequence is significant?

we have discovered a DNA sequence repeated through our genome. We have also discovered this sequence in closely related species. I am wondering what are the mathematical approaches that I may use...

06 June 2016 3,061 2 View

How to set the treeing parameter in PhyML after I get the the most appropriate tree from jmodeltest2?

suppose the running of jmodeltest2 come up the best model for my nucleotide alignment is as follow: Best model = 010231+I+G+F f(a) = 0.24 f(c) = 0.41 f(g) = 0.26 f(t) =...

06 June 2016 1,759 0 View

Anyone know of an algorithm to programmatically rearrange a phylogenetic tree upon rooting on a given branch?

Our program already produces a tree. We would like to allow the user the choice to root the tree on an external or internal branch, but the resulting change in the tree needs to be coded - and we...

06 June 2016 7,189 14 View

Will the topology of a phylogenetic tree change after removing a number of sequences and re-run the treeing method?

Hello, suppose I have constructed a phylogenetic tree with all OTU sequences and reference sequences. I now want to have a tree containing only the OTU sequences. Is it a good practical to remove...

06 June 2016 3,725 5 View

From the MrBayes tree output files, which trees other than .con.tre file can be used?

Hello everyone, I am a very new user of MrBayes 3.2. Please help with my doubt. I have constructed a phylogenetic tree of 43 sequences using MEGA and MrBayes. I have attached both the files here....

06 June 2016 7,441 3 View

Can anybody suggest me exact analysis of neighbor joining dendrogram of bacterial population?

Can anybody suggest me exact analysis of neighbor joining dendrogram of bacterial population? In this regards file attached.

06 June 2016 8,814 2 View

What are "Unverified" sequence in Genebank? Can I take those unverified sequences from Genebank for my phylogenetic analysis?

I am working on molecular phylogeny in the order level. When I am extracting the sequences from NCBI Genebank, I found there are lot sequences marked as unverified. For concratenation of multiple...

25 May 2016 2,652 7 View

Why the phylogenetic tree do not have bootstrap value (the NA value showed in the phylogenetic tree).

I am doing phylogenetic analysis and get the result as you can see in the attached photo. The bootstrap value in the phylogenetic tree is NA. It means that does not have bootstrapping values. But...

25 May 2016 8,397 3 View

Why are monocots and dicots mixed in the phylogeny tree?

Dear colleagues, My colleague and I cloned a gene from sword bean which is mainly expressed in flower. After I did blast using the protein's amino acid sequence, I found there are just 250...

23 May 2016 7,818 9 View

How to explain diversity indices?

I am having a hard time explaining diversity indices of my 454 data e.g. PD whole tree, Chao1, Observed species, Shannon, Simpson.. I wonder if someone may give brief overview of indices or may...

05 May 2016 2,957 3 View

What are genes which are suitable for phylogenetic tree construction and compare simultaneously the phylogeny at gene and protein level ?

Our concern is only at species level, but we are interested in the amount of conservation that happens at protein level across species when compared with gene level

05 May 2016 8,258 3 View

Why are monocots and dicots mixed in the phylogeny tree?

Dear colleagues, My colleague and I cloned a gene from sword bean which is mainly expressed in flower. After I did blast using the protein's amino acid sequence, I found there are just 250...

05 May 2016 3,164 10 View

Why the phylogenetic tree do not have bootstrap value (the NA value showed in the phylogenetic tree).

I am doing phylogenetic analysis and get the result as you can see in the attached photo. The bootstrap value in the phylogenetic tree is NA. It means that does not have bootstrapping values. But...

05 May 2016 6,179 3 View

Input matrix for Splitstree for Dominant markers using binary data ?

I am working on conservation genetics of some alpine medicinal plants. I have used some dominant markers and co-dominant markers. I am unable to construct network tree by using Splitstree. Can...

05 May 2016 1,056 4 View

What are "Unverified" sequence in Genebank? Can I take those unverified sequences from Genebank for my phylogenetic analysis?

I am working on molecular phylogeny in the order level. When I am extracting the sequences from NCBI Genebank, I found there are lot sequences marked as unverified. For concratenation of multiple...

05 May 2016 6,471 7 View

Somebody knows if in BPEC (Bayesian Phylogeographic and Ecological Clustering) contours obtained represents samples or posterior probabilities?

I made a bayesian analyse with BPEC, and I obtained some contour files that I can visualize in Google Earth. I would know if this contours represents my sample sites or posterior probabilities. I...

26 April 2016 4,017 2 View

How to remove introns from DNA sequences extracted from GenBank like the nuclear protein gene EF-1a ?

Which software can be used for this issue? Is it important to remove introns from DNA sequence when we want to establish a phylogenetic tree from several genes with a Maximum Likelihood inference...

20 April 2016 335 3 View

How can I construct a phylogenetic tree?

Need step by step guideline to construct a 16SrRNA phylogenetic tree using MEGA /NCBI-BLAST.

04 April 2016 9,422 6 View

Somebody knows if in BPEC (Bayesian Phylogeographic and Ecological Clustering) contours obtained represents samples or posterior probabilities?

I made a bayesian analyse with BPEC, and I obtained some contour files that I can visualize in Google Earth. I would know if this contours represents my sample sites or posterior probabilities. I...

04 April 2016 7,450 2 View

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