Hi, I am trying to confirm the bacterial isolates by sequencing. I have targeted lytA gene in Streptococcus pneumoniae. I completed the alignment using CLUSTALW. Now I would like to analyse the sequences by phylogenetic methods, so as to confirm whether any isolate is S.pneumoniae or not. I found that two of the papers attached below, used two different methods - Maximum Likelihood and Maximum Parsimony. I am doing this for the first time, and so I couldn't decide which method to follow. Kindly tell me which method should I use and how to interpret the tree results. Thank you.
Hi,
We looking for methods could be more supporting and both Maximum Likelihood and Maximum Parsimony well recommended for stronger phylogenetic tree. Plase have a look for the link below may help you make you decision? Good luck
Ali
https://www.researchgate.net/post/What_is_the_best_choice_between_Maximum_Likelihood_and_Bayesian_Inference_for_inferring_phylogenetic_relationships_especially_at_low-taxonomic_levels
https://mbe.oxfordjournals.org/content/20/2/248.full
https://www.researchgate.net/post/Neighbor_joining_or_maximum_likelihood/1
Dear Murthy
Every method has some advantages as well as disadvantages. Both Maximum Likelihood and Maximum Parsimony methods are character based methods. If you are using species of same genus, then I prefer you to use Maximum Parsimony method using p-distance. Maximum Likelihood can be an alternate when a problem cannot be solved with Maximum Parsimony. Use both methods, and see which tree fits best as far as your study is concerned. Use pairwise deletion, and 1000 bootstrap values in the options provided in different softwares like Mega, Phylip, etc. I prefer you to use Mr. Bayers for the phylogeny
Dear Murthy
Both these methods are used for drawing phylogenetic trees. Maximum parsimony and Maximum likehood methods are character based tree searching methods. If you are performing phylogeny among species of same genus, then I prefer you to use Maximum Parsimony and Minimum Evolution method. MP and ML methods have advantages as well as disadvantages, Maximum Likelihood can be an alternate when a problem cannot be solved with Maximum Parsimony. I also prefer you to use MrBayes which is free software program.
If you need further information, you are free to ask.
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