Hi
I recently started working on phylogenetic analysis. I made a tree the picture is attached below. What does number indicates at nodes of the tree. What more inference can I draw from the tree. How could I learn more about phylogenetic analysis (any book), please give your valuable suggestion.
those numbers are bootstrap values provided the test of phylogeny you had set was bootstrap method. u can check the parameters of your tree. if the number of bootstrap replications was set 100 n you see 65-90 as the number on the branch of the tree then it means your tree is reliable.
Numbers at nodes can mean more than one thing. In your case, it's probably support values, given as %. See one quick explanation at http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
while keeping in mind it's not a % in their example, so you'd multiply their values by 100 to compare them with yours.
For the exact answer a bit more detailed description of your analysis needed. Which software, which method etc. was used.
I am analyzing a protein in fungi kingdom and I want to prove the divergence as well as convergence of the same protein within the kingdom as well as other. Right now I am using Mega 7 software. As I am doing it for the first time, I do not know what are the inference can I able to draw by phylogenetic analysis and how? the uploaded sequence I did with maximum likelihood method.
those numbers are bootstrap values provided the test of phylogeny you had set was bootstrap method. u can check the parameters of your tree. if the number of bootstrap replications was set 100 n you see 65-90 as the number on the branch of the tree then it means your tree is reliable.
Dear Qurshid,
In this case these numbers on the branches represent bootstrap support (branch support). According to your analysis the five last branches form a well supported monophyletic clade (i.e. they most probably share a common ancestor).
probably bootstrap;
I think "Tree Thinking: An Introduction to Phylogenetic Biology, by David A. Baum and Stacey D. Smith" is a very good book for beginners in phylogenetic research.
Thank you very much sansrity, csaba, and xiong. I have used protein for phylogenetic analysis, I used n=500 bootstrap replication. What should be the minimum criteria for phylogenetic analysis utilizing maximum likehood method and how many bootstrap replication to be taken into account.
They are Jackknifes/ Bootstraps depend to your tree generating method. in both cases this numbers show you, how your clade supported by final tree.
note that the numbers below 50 does not show in your final tree.
in a simple word; software generate a numbers of trees (i.e 1000000) and save them into your PC/Laptop RAM, then all trees compare and a final tree show as result. so you can suppose that this numbers is a mean of generated trees. i.e 64 means that 64% of your total trees was like that you see now!
it is better use at least 1000 generations for your tests.
Salem, Mr Hasan
For reading I recommend you my doctoral thesis https://www.researchgate.net/profile/Semir_Bechir_Suheil_Gaouar. For numbers that you track on your phylogenetic tree, this is the number of times the relationship at the node between taxa study emerged during the resampling technique or sometimes it is a percentage of appearance of node. it is you who determine when analyzing by the software required number of resampling (usually one chosen 1000). If these numbers are lower than 95% it means that the risk of accepting the node it's significant and you can not acept this relation in this node.
The number above the nodes indicate bootstrap value. It represents the phylogenetic confidence of the the tree topology. Normally bootstrap value above 70 is considered a plausible score for branch validation. MEGA is not a good software for such studies, opt for BEAST/PAUP/PHYLIP to get precise tree topology. You can also try CLC genomics. Good luck.
Hi@Qurshid Hasan Khan.. i came across your earlier question in my search for similar answers. May i know if you have finally found some sort of answer to that doubt? As a novice also, i am a bit out of sorts with this too...how to describe my tree.. any suggestions would be much appreciated. thanks... and any others who have suggestions as well.
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