For sequences that have ________ a phylogenetic analysis is __________

diverged considerably, more challenging

diverged considerably, less challenging

diverged considerably, a less work to do

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

sometimes contradicting, are constant

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

NEIGHBOR estimates phylogenies using the neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA)

FITCH estimates a phylogenetic tree assuming additivity of branch lengths

FITCH uses the Fitch-Margoliash method

FITCH assumes a molecular clock but KITSCH does not

NEIGHBOR estimates phylogenies using the neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA)

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

It is especially suitable when the rate of evolution of the separate lineages under consideration varies

It is very much like the Fitch-Margoliash method

It is totally dissimilar than the Fitch-Margoliash method

It is especially suitable when the rate of evolution of the separate lineages under consideration varies

When the branch lengths of trees of known topology are allowed to vary in a manner that simulates varying levels of evolutionary change, it is the most reliable method

A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

The underlying mutational theory is like those used to produce the PAM matrices for predicting changes in DNA and protein sequences

This method is different from the Smith-Waterman local alignment algorithm

This method is quite similar to the Smith-Waterman local alignment algorithm

The underlying mutational theory is like those used to produce the PAM matrices for predicting changes in DNA and protein sequences

Sequences are predicted to change by a Markov process such that each mutation in the sequence is independent of previous mutations at that site or at other sites

Which of the following is incorrect about Caveats?

Unusually high GC content in the original dataset is the potential cause for generating biased trees

Unusually accelerated evolutionary rates is the potential cause for generating biased trees

Unusually accelerated evolutionary rates is the potential cause for generating biased bootstrap estimates

Not a large number of bootstrap re-sampling steps are needed to achieve yielding results

Which of the following is wrong statement about the maximum likelihood approach?

It finds a tree that best accounts for the variation in a set of sequences

This method doesn’t always involve probability calculations

It finds a tree that best accounts for the variation in a set of sequences

The method is similar to the maximum parsimony method

The analysis is performed on each column of a multiple sequence alignment

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

PHYLIP includes mentioned two programs for this maximum likelihood analysis

DNAML estimates phylogenies from nucleotide sequences by the maximum likelihood method

DNAMLK estimates phylogenies in the same manner as DNAML

DNAMLK estimates phylogenies without molecular clock

Phylogenetic analysis of a set of sequences that aligns ______ is straightforward because the positions that correspond in the sequences can be readily identified in a ______ of the sequences.

in a haphazard manner, multiple sequence alignment

very well, multiple sequence alignment

in a haphazard manner, multiple sequence alignment

in a distorted way, multiple sequence alignment

Which of the following is untrue regarding the distance methods?

On a tree, these sequences share a node or common ancestor position and are each joined to that node by a branch

The sequence pairs that have the largest number of sequence changes between them are termed ‘neighbors’

On a tree, these sequences share a node or common ancestor position and are each joined to that node by a branch

It produces a phylogenetic tree of the group

It employs the number of changes between each pair in a group of sequences

Which of the following is incorrect statement about branch-and-bound?

It starts by building a distance tree for all taxa involved

It uses a shortcut to find an MP tree

It establishes an upper limit (or upper bound) for the number of allowed sequence variations

It starts by building a distance tree for all taxa involved

Which of the following is incorrect statement about Tree-Searching Methods?

The choice of the first three taxa can be random

Parsimony method examines all possible tree topologies to find the maximally parsimonious tree

It starts by building a three taxa unrooted tree, for which only one topology is available

This is different than exhaustive search method

Corrects for unequal evolutionary rates between sequences by using a conversion step. This conversion requires the calculations of “r-values” and “transformed r-values” using the following formula ______

dᴀʙ’ = dᴀʙ − 1/3 × (rᴀ + rʙ)

dᴀʙ’ = dᴀʙ − 1/4 × (rᴀ + rʙ)

dᴀʙ’ = dᴀʙ − 1/2 × (rᴀ + rʙ)

dᴀʙ’ = dᴀʙ − 1/3 × (rᴀ + rʙ)

dᴀʙ’ = (dᴀʙ/3) − 1/2 × (rᴀ + rʙ)

Which of the following is untrue about distance based methods?

The clustering-type algorithms compute a tree based on a distance matrix starting from the most similar sequence pairs

The computed evolutionary distances can be used to construct a matrix of distances between all individual pairs of taxa

Clustering is the only method among the algorithms for the distance-based tree-building method

The clustering-type algorithms compute a tree based on a distance matrix starting from the most similar sequence pairs

Based on the pairwise distance scores in the matrix, a phylogenetic tree can be constructed for all the taxa involved

Which of the following is untrue about the Optimality-Based Methods?

Optimality-based methods select a tree that best fits the actual evolutionary distance matrix

The clustering-based methods produce multiple trees as output

Optimality-based methods select a tree that best fits the actual evolutionary distance matrix

There is no criterion in judging how this tree is compared to other alternative trees

Optimality-based methods have a well-defined algorithm to compare all possible tree topologies

Which of the following is incorrect about nonparametric bootstrapping?

Certain sites are randomly replaced by other existing sites

A new multiple sequence alignment of the same length is generated with random duplication of some of the sites

A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites

Certain sites are randomly replaced by other existing sites

Certain sites may appear multiple times, and other sites may not appear at all in the new alignment

Which of the following is untrue regarding the distance methods?

The distance method was pioneered by Feng and Doolittle

A collection of programs by authors Feng and Doolittle will produce both an alignment and tree of a set of protein sequences

The program CLUSTALW uses the neighbor-joining distance method as a guide to multiple sequence alignments

Among the Programs of the PHYLIP package, DNADIST is not one of them

Which of the following is untrue about the Unweighted Pair Group Method Using Arithmetic Average?

The distances between this new composite taxon and all remaining taxa are calculated to create a reduced matrix

The simplest clustering method is UPGMA, which builds a tree by a sequential clustering method

Given a distance matrix, it starts by grouping two taxa with the largest pairwise distance in the distance matrix

The distances between this new composite taxon and all remaining taxa are calculated to create a reduced matrix

The grouping process is repeated and another newly reduced matrix is created

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

This method predicts the evolutionary tree

It minimizes the number of steps required to generate the observed variation in the sequences

The method is also sometimes referred to as the minimum evolution method

Only a pairwise sequence alignment is required to predict which sequence positions are likely to correspond

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

Those trees that produce the smallest number of changes overall for all sequence positions are identified

The analysis steps are continued for every position in the sequence alignment

This method is used for large numbers of sequences

Those trees that produce the smallest number of changes overall for all sequence positions are identified

This method is used for sequences that are quite similar

In the bootstrap method, the data are resampled by _____ choosing _____ columns from the aligned sequences to produce, in effect, a new sequence alignment of the _____

randomly, vertical, different lengths

randomly, horizontal, same length

specifically, vertical, different lengths

randomly, vertical, same length

randomly, vertical, different lengths

Which of the following is incorrect about Bayesian Simulation?

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

It does not require bootstrapping

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

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

Which of the following is wrong statement about the maximum likelihood method’s steps?

The set of sequences is then aligned

It starts with an evolutionary model of sequence change that provides estimates of rates of substitution of one base for another

In the beginning there is an evolutionary model of sequence change that provides estimates of transitions and transversions in a set of nucleic acid sequences

The rates of all possible substitutions are chosen so that the base composition differs

The set of sequences is then aligned

In Jukes–Cantor Model to correct evolutionary distances, A formula for deriving evolutionary distances that include hidden changes is introduced by using a logarithmic function. It is ____

dᴀʙ = −(3/4) log[1 − (4/7)ₚᴀʙ]

dᴀʙ = −(3/4) ln[1 − (5/3)ₚᴀʙ]

dᴀʙ = −(3/4) log[1 − (4/3)ₚᴀʙ]

dᴀʙ = −(3/4) ln[1 − (4/3)ₚᴀʙ]

101 + Mcqs in Phylogenetic Programs in Bioinformatics Page 1 McqOptions

1.	Neighbor-joining chooses the sequences that should be joined to give the best least squares estimates of the branch lengths that most closely reflect the actual distances between the sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

2.	For sequences that have ________ a phylogenetic analysis is __________
A.	diverged considerably, more challenging
B.	not diverged, more challenging
C.	diverged considerably, less challenging
D.	diverged considerably, a less work to do
Answer» B. not diverged, more challenging

3.	The KH test sets out to test the null hypothesis that the two competing tree topologies are not significantly different.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

4.	Parsimony can give ________ information when rates of sequence change _______ in the different branches of a tree that are represented by the sequence data.
A.	misleading, vary
B.	useful, change
C.	misleading, are constant
D.	sometimes contradicting, are constant
Answer» B. useful, change

6.	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.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

9.	MrBayes is a Bayesian phylogenetic inference program.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

10.	Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

16.	The main disadvantage of maximum likelihood methods is that they are _____
A.	mathematically less folded
B.	mathematically less complex
C.	computationally lucid
D.	computationally intense
Answer» E.

18.	The branch-and-bound method starts building trees in a similar way as in the exhaustive method.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

20.	In a heuristic tree search, only a small subset of all possible trees is examined.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

21.	DNA sequences are sometimes more biased than protein sequences because of preferential codon usage in different organisms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

22.	In many cases ______ sequences are preferable to ______ sequences because they are relatively ____ conserved.
A.	protein, nucleotide, less
B.	nucleotide, protein, less
C.	protein, nucleotide, more
D.	nucleotide, protein, more
Answer» D. nucleotide, protein, more

33.	In PHYML, The tree searching _____ when the total ML score no longer ______
A.	ceases, increases
B.	stops, decreases
C.	terminates, decreases
D.	stops, increases
Answer» E.

23.	Protein sequences can remain the same while the corresponding DNA sequences have more room for variation.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

24.	In the final steps of the bootstrap method, the _____ the decay value, the _______ significant the original branches.
A.	greater, less
B.	greater, more
C.	lesser, more
D.	more, less
Answer» C. lesser, more

25.	Tracking the evolutionary history of individual genes in a group of species can reveal which genes have remained in a genome for a long time and which genes have been horizontally transferred between species.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

26.	Two more recent uses of phylogenetic analysis are to analyze ______ and to trace the evolutionary history of specific genes. Which of the following could not be the correct blank?
A.	gene families
B.	genomes
C.	proteomes
D.	physical separation methods
Answer» E.

27.	The traditional use of phylogenetic analysis is to discover evolutionary relationships among species.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

30.	The basic assumption of the UPGMA method is that all taxa evolve at a constant rate and that they are equally distant from the root, implying that a molecular clock is in effect.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

32.	Minimum evolution (ME) constructs a tree with a similar procedure, but uses a different optimality criterion that finds a tree among all possible trees with a minimum overall branch length. The optimality criterion relies on the formula S = ∑bi where bi is the (i)th branch length.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

35.	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.
A.	multiplied
B.	added
C.	divided
D.	squared
Answer» B. added

40.	A common recommendation is to use at least two of the methods—maximum parsimony, distance, or maximum likelihood, for the analysis.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

42.	In the bootstrap method, for branches in the predicted tree topology to be significant, the resampled data sets should frequently predict the same branches.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Neighbor-joining chooses the sequences that should be joined to give the best least squares estimates of the branch lengths that most closely reflect the actual distances between the sequences.

For sequences that have ________ a phylogenetic analysis is __________

The KH test sets out to test the null hypothesis that the two competing tree topologies are not significantly different.

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

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

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

A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

MrBayes is a Bayesian phylogenetic inference program.

Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.

Which of the following is incorrect about Caveats?

Which of the following is wrong statement about the maximum likelihood approach?

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

Phylogenetic analysis of a set of sequences that aligns ______ is straightforward because the positions that correspond in the sequences can be readily identified in a ______ of the sequences.

Which of the following is untrue regarding the distance methods?

The main disadvantage of maximum likelihood methods is that they are _____

Which of the following is incorrect statement about branch-and-bound?

The branch-and-bound method starts building trees in a similar way as in the exhaustive method.

Which of the following is incorrect statement about Tree-Searching Methods?

In a heuristic tree search, only a small subset of all possible trees is examined.

DNA sequences are sometimes more biased than protein sequences because of preferential codon usage in different organisms.

In many cases ______ sequences are preferable to ______ sequences because they are relatively ____ conserved.

Protein sequences can remain the same while the corresponding DNA sequences have more room for variation.

In the final steps of the bootstrap method, the _____ the decay value, the _______ significant the original branches.

Tracking the evolutionary history of individual genes in a group of species can reveal which genes have remained in a genome for a long time and which genes have been horizontally transferred between species.

Two more recent uses of phylogenetic analysis are to analyze ______ and to trace the evolutionary history of specific genes. Which of the following could not be the correct blank?

The traditional use of phylogenetic analysis is to discover evolutionary relationships among species.

Corrects for unequal evolutionary rates between sequences by using a conversion step. This conversion requires the calculations of “r-values” and “transformed r-values” using the following formula ______

Which of the following is untrue about distance based methods?

The basic assumption of the UPGMA method is that all taxa evolve at a constant rate and that they are equally distant from the root, implying that a molecular clock is in effect.

Which of the following is untrue about the Optimality-Based Methods?

Minimum evolution (ME) constructs a tree with a similar procedure, but uses a different optimality criterion that finds a tree among all possible trees with a minimum overall branch length. The optimality criterion relies on the formula S = ∑bi where bi is the (i)th branch length.

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

Which of the following is incorrect about nonparametric bootstrapping?

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.

Which of the following is untrue regarding the distance methods?

Which of the following is untrue about the Unweighted Pair Group Method Using Arithmetic Average?

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

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

A common recommendation is to use at least two of the methods—maximum parsimony, distance, or maximum likelihood, for the analysis.

In the bootstrap method, the data are resampled by _____ choosing _____ columns from the aligned sequences to produce, in effect, a new sequence alignment of the _____

In the bootstrap method, for branches in the predicted tree topology to be significant, the resampled data sets should frequently predict the same branches.

The choice of a suitable multiple sequence alignment method depends on the degree of variation among the sequences.

Which of the following is incorrect about Bayesian Simulation?

In the Neighbor Joining step, The UPGMA method uses unweighted distances and assumes that all taxa have constant evolutionary rates.

The tree construction process is somewhat similar to that used UPGMA.

A generalized expression of the r-value is ri calculated based on the following formula _______

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.

Which of the following is wrong statement about the maximum likelihood method’s steps?

In Jukes–Cantor Model to correct evolutionary distances, A formula for deriving evolutionary distances that include hidden changes is introduced by using a logarithmic function. It is ____

For sequences that have a phylogenetic analysis is __

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

Phylogenetic analysis of a set of sequences that aligns is straightforward because the positions that correspond in the sequences can be readily identified in a of the sequences.

In many cases sequences are preferable to sequences because they are relatively conserved.

In the final steps of the bootstrap method, the _ the decay value, the ___ significant the original branches.

In PHYML, The tree searching _ when the total ML score no longer __

In the bootstrap method, the data are resampled by ___ choosing _ columns from the aligned sequences to produce, in effect, a new sequence alignment of the ___

44.	Which of the following is incorrect about Bayesian Simulation?
A.	It does not require bootstrapping
B.	It requires bootstrapping
C.	The MCMC procedure itself involves thousands or millions of steps of resampling
D.	Posterior probabilities are assigned at each node of a best Bayesian tree as statistical support
Answer» C. The MCMC procedure itself involves thousands or millions of steps of resampling

47.	A generalized expression of the r-value is ri calculated based on the following formula _______
A.	ri = ∑dij + dj²
B.	ri = ∑dij
C.	ri = ∑dij + di
D.	ri = ∑dij + dj
Answer» C. ri = ∑dij + di