Hello,
Please write me what kind of phylogenetic tree is showed on my picture. What do mean the values following names of aligned sequences?
I will be very grateful for any help.
I believe this is a cladogram due to the equal lengths of the branches from the left to the right. A true phylogenetic tree also contains information about how different taxa in the tree are i.e. have different branch lengths. The tree also appears to be unrooted.
It might help, if you were able to say more about where the tree came from and how it was derived.
Assuming that you have used ebi clustal tools for phylogenetic tree construction, I would say the values corresponds to the branch lengths since clustal uses distance based methods . Each branch length corresponds to the rate of evolution. Since this is a cladogram the branch lengths are equal and usually branch orders are used for interpretation.
If you have used some other tool please do let us know that along with the tree construction algorithm you have used.
I used Clustal software. I there possibility to estimate phylogenetic distances on the basis of these values? I was asked about it and I did not know what to answer.
Josh, my guess this is a guide tree which is the first step to align multiple sequences in Clustal and describes the approximate relationships of the sequences to each other. It is constructed from the distance matrix (from all versus all pairwise alignments). Then the sequences are progressively aligned according to the hiearchy in this guide tree. This dendogram is saved in ".dnd" file, while the actual MSA is in ".aln".
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You have a polytomy. http://en.wikipedia.org/wiki/Polytomy. Amidostomum is a nematode. Thats about all you can say without more information.
Do you know the meaning of values following the names. Is there a possibility to estimate phylogenetic distances on the basis of these values?
You tell us what the numbers after the names mean. You showed us a cladogram with four taxa and no real phylogenetic resolution. How did you do the analysis? Are these strain numbers? Branch distances? We can't help you if you don't give us any information on your phylogenetic analysis and why you did what you did.