Hi Nur Fatihah Hasan

In a very simple sense....Many phylogenetic approaches or algorithms ( and also those used in sequence analysis in bioinformatics) if used as such they are computationally exhaustive ..as the sample/sequence number or length of sequences increase .....Even while doing phylogenetic analysis...after a certain sample number the permutations/combinations of possible trees becomes so large that even on most of the regularly used PCs it would be impossible to do it.....

heuristic/fast approaches are approximation of the basic algorithms to do the analysis quickly......for you sample size of 9 ...it should be possible to do exhaustive analysis instead of heuristic analysis

bye

Hi there,

When doing exaustive search for trees, your computer will keep in memory all the possible combinations of branching patterns among your OTU (Operational Taxonomic Units).

For example, if you have three OTU, there is only one possible branching pattern. If you have four OTU there are three possible topologies (different trees). With five OTUs there are 32 possible trees, and with 10 OTU the total number of possible trees will be 2K. Beyond 11 OTUs it is not feasible to compute all topologies in the search for the optimal tree, therefore, the heuristic searches are used.

With nine OTUs it will be possible, to use an exaustive search. If you use heuristic searches, these do not guarantee that the most optimal tree is found, and there are many algorithms that try to improve the search making subsamples among the possible topologies.

The commands to make any search using any of the strategies will vary from software to software.

good luck

Thanks Ajay Saini and Carlos Figueiredo. I will re-run the analysis using exhaustive search. cheers..

There is no reason not to use exhaustive search on nine taxa.