Is bootstrap necessary for the construction of phylogenetic tree and what is the best no. of bootstrap replicates value for construction of bacterial phylogenetic tree by any method?
I have seen several bootstrap values like 100, 500 and 1000 etc., at elsewhere. what parameters I should select before constructing a phylogenetic tree and which software is best for it ? please let me know in detail .
The bootstrapping value doesn't say anything direct about evolutionary conservation: it says how well this node is supported in the model you're using to generate a phylogenetic tree. Bootstrapping is a procedure where you take a random subset of the data and re-run the phylogenetic analysis, and the reported value is the percentage of bootstrap replicates in which the node showed up. Thus, 100 means that the node is well-supported: it showed up in all bootstrap replicates. In common language it can be say that Bootstrapping values is nothing but the confidence of the clades which are joined together. For the construction of phylogenetic tree I will suggest you to use MEGA which is more reliable, open source and very important user-friendly tool else there are more option for the construction like Clustalx, Phylip etc.
Bootstrapping value may or may not have implications upon evolutionary aspects of a phylogram. The main significance of Bootstrap value is look for reliability of any branch or node in a phylogram where by different subset from your data are checked for redundancy. For e.g. 100 out of 100 value for a clade will reflect a very high confidence whereas , a lower value will have low confidence.
For Software there are numerous, you can try MEGA, Mesquite, SeaView (a simple tool) Unipro Ugene, etc. There are online tools as well. MEGA is one of the best tools available with awesome analysis option, but you can explore Mesquite as well. Hope this helps.
Regards
Pankaj
The concept of Bootstrapping is quite straightforward. It means that the analyses are repeated using a part of the dataset (subsampling). It is used as a support value in phylogenetic analyses such as Maximum Likelihood and the interpretation is very easy: you repeat the analyses (e.g.) 100 times, each time discarding a part of the dataset (let's say a part of the sequences) and you see how many times out of 100, you get the same branch. Low Bootstrap supports indicate that only a part of your "sequence" is responsible for "grouping" the terminals in a given branch.
- Badges
- Science topic
- Similar topics
- Statistics
- Time Series