Bioinformatics Practice Test 7

1. Once all positions in the sequence alignment have been examined, the likelihoods given by each column in the alignment for each tree are _____ to give the likelihood of the tree.

divided

multiplied

added

squared

2. A gene phylogeny only describes the evolution of a particular gene or encoded protein.

False

True

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

False

True

4. Which of the following is incorrect about Bayesian Simulation?

It requires bootstrapping

The MCMC procedure itself involves thousands or millions of steps of resampling

It does not require bootstrapping

Posterior probabilities are assigned at each node of a best Bayesian tree as statistical support

5. Evolution of a particular sequence _______ correlate with the evolutionary path of the species.

does not necessarily

always

does not

invariably

6. Which of the following is incorrect about Bootstrapping?

It does the tests by repeatedly sampling trees through slightly perturbed datasets

The robustness of the original tree can be assessed here

A newly constructed tree is not biased at all

It is a statistical technique that tests the sampling errors of a phylogenetic tree

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

phylogenetic, GA (Genetic Algorithm)

sequence based alignment, dynamic programming

sequence based alignment, GA (Genetic Algorithm)

phylogenetic, dynamic programming

8. In about the maximum likelihood approach, for each tree, the number of sequence changes or mutations that may have occurred to give the sequence variation is considered.

False

True

9. Which of the following is wrong statement about DNAML and DNAMLK?

DNAML estimates phylogenies from nucleotide sequences by the maximum likelihood method

PHYLIP includes mentioned two programs for this maximum likelihood analysis

DNAMLK estimates phylogenies in the same manner as DNAML

DNAMLK estimates phylogenies without molecular clock

10. It can be computationally very demanding to find a true phylogenetic tree when the number of sequences is large.

True

False