Q. In Shimodaira–Hasegawa Test, The degree of freedom used for the analysis depends on the substitution model used. It relies on the following test formula d = 2(ln LA – ln LB) = 2 ln(LA/LB). Here, is the log likelihood ratio score and ln LA and ln LB are likelihood scores for tree A and tree B, respectively.

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Q. PAUP is a Macintosh program (UNIX version available in the GCG package) with a very user-friendly graphical interface.

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Q. In PAUP, the distance options include NJ, ME, FM, and UPGMA.

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Q. Phylip stands for Phylogenetic inference package (by Joe Felsenstein).

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Q. In PAUP, to complete an analysis the user is not required to move between different subprograms while keeping modifying names of the intermediate output files.

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Q. Which of the following is untrue regarding TREE-PUZZLE?

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Q. Which of the following is untrue regarding TREE-PUZZLE?

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Q. PHYML is a web-based _______ program using the _____

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Q. In PHYML, The tree searching _____ when the total ML score no longer ______

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Q. MrBayes is a Bayesian phylogenetic inference program.

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Q. MrBayes has a range of probabilistic models available to search for a set of trees with the lowest posterior probability.

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Q. Which of the following is untrue regarding the maximum parsimony method?

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Q. Which of the following is untrue regarding the maximum parsimony method?

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Q. Which of the following is untrue regarding the programs for analysis of nucleic acid sequences?

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Q. PROTPARS counts the minimum number of mutations to change a codon for the first amino acid into a codon for the second amino acid, but only scores those mutations in the mutational path that actually change the amino acid.

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Q. Parsimony can give ________ information when rates of sequence change _______ in the different branches of a tree that are represented by the sequence data.

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Q. Which of the following is untrue regarding the distance methods?

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Q. Which of the following is untrue regarding the distance methods?

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Q. Which of the following is untrue regarding the Distance analysis programs in PHYLIP?

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Q. Which of the following is untrue regarding the neighbor-joining method?

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