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

DNAPARS treats gaps as a fifth nucleotide state

DNAPENNY performs parsimonious phylogenies by branch-and-bound search

DNAPENNY can analyze sequences up to 11 or 12

Compatibility criterion is not involved in DNACOMP

Which of the following is incorrect statement about Maximum Parsimony Method?

In dealing with problems that may have an infinite number of possible solutions, choosing the simplest model may help to ‘cut off’ those variables that are not really necessary to explain the phenomenon

By cutting off the unnecessary variables, model development may become difficult, and there may be more chances of introducing inconsistencies, ambiguities, and redundancies, hence, the name Occam’s razor

In dealing with problems that may have an infinite number of possible solutions, choosing the simplest model may help to ‘cut off’ those variables that are not really necessary to explain the phenomenon

This method chooses a tree that has the fewest evolutionary changes or shortest overall branch lengths

It is based on a principle related to a medieval philosophy called Occam’s razor

Which of the following is incorrect statement about Character-based methods?

They may avoid the loss of information when characters are converted to distances

They are also called discrete methods

They are based directly on the sequence characters rather than on pairwise distances

They doesn’t count mutational events accumulated on the sequences

They may avoid the loss of information when characters are converted to distances

Which of the following is incorrect statement about Building Work of MP tree?

It works by searching for all possible tree topologies and reconstructing ancestral sequences that require the minimum number of changes to evolve to the current sequences

Other than informative sites are non-informative, which are constant sites or sites that have changes occurring only once

Informative sites are the ones that can often be explained by a unique tree topology

Constant sites have the same state in all taxa and are quite useful in evaluating the various topologies

Which of the following is incorrect regarding the terminologies of phylogenetics?

The lines in the tree are called branches

The connecting point where two adjacent branches join is called a node

Node represents an inferred ancestor of extant taxa

At the tips of the branches are long lost species or sequences

The lines in the tree are called branches

Which of the following is incorrect regarding the terminologies of phylogenetics?

Lineage is often synonymous with a tree branch leading to a defined monophyletic group

A group of taxa descended from a single common ancestor is defined as a clade or monophyletic group

In a monophyletic group, two taxa share a unique common ancestor shared by other taxa as well

Lineage is often synonymous with a tree branch leading to a defined monophyletic group

When a number of taxa share more than one closest common ancestors, they do not fit the definition of a clade. In this case, they are referred to as paraphyletic

Which of the following is incorrect statement?

One criticism of this approach is that the size of datasets has been changed into one half and that the datasets are no longer considered replicates

In this method one half of the sites in a dataset are randomly deleted

It creates datasets half as long as the original

Each new dataset is subjected to phylogenetic tree construction using the different methods as the original

One criticism of this approach is that the size of datasets has been changed into one half and that the datasets are no longer considered replicates

Which of the following is incorrect regarding the terminologies of phylogenetics?

An unrooted phylogenetic tree does not assume knowledge of a common ancestor

The branching pattern in a tree is called tree topology

When all branches bifurcate on a phylogenetic tree, it is referred to as dichotomy

In case of dichotomy, each ancestor divides and gives rise to multiple descendants

An unrooted phylogenetic tree does not assume knowledge of a common ancestor

Which of the following is untrue regarding TREE-PUZZLE?

Because of the heuristic nature of the program, it allows ML analyses of large datasets

It is a program performing quartet puzzling

It allows various substitution models for likelihood score estimation

It doesn’t incorporate a discrete γ model

Because of the heuristic nature of the program, it allows ML analyses of large datasets

Which of the following is incorrect about Bootstrapping?

The robustness of the original tree can be assessed here

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

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

A newly constructed tree is not biased at all

The robustness of the original tree can be assessed here

For unrooted trees, the number of unrooted tree topologies (NU) is ________

NU = (2n− 5)!/2ⁿ⁻³(n− 5)!

NU = (2n− 5)!/2ⁿ⁻³(n− 3)!

Which of the following is incorrect statement about Molecular Markers?

The decision to use nucleotide or protein sequences depends on the purposes of the study

For studying very closely related organisms, protein sequences are preferred

The decision to use nucleotide or protein sequences depends on the purposes of the study

For constructing molecular phylogenetic trees, one can use either nucleotide or protein sequence data

The decision to use nucleotide or protein sequences depends on the properties of the sequences

Which of the following is untrue about the Fitch–Margoliash?

Method selects a best tree among all possible trees based on minimal deviation between the distances calculated in the overall branches in the tree and the distances in the original dataset

It starts by randomly clustering two taxa in a node

It starts by creating three equations to describe the distances

The method searches for some specific tree topologies

The species evolution is the ______ of evolution by _____ in a genome.

combined result, multiple genes

It is often desirable to define the root of a tree. There are two ways to define the root of a tree. One is to use an outgroup, which ______

is a sequence that is homologous to the sequences under consideration

is separated from those sequences at an early evolutionary time

is generally determined from independent sources of information

is generally determined from similar or related sources of information

The number of rooted trees (NR) for n taxa is ______

NR = (2n− 3)!/2ⁿ⁺² (n− 2)!

NR = (2n− 3)!/2ⁿ⁻² (n− 5)!

NR = (2n− 3)!/2ⁿ⁻² (n− 2)!

Which of the following is incorrect statement about Choosing Substitution Models?

The evolutionary divergence is beyond the ability of the statistical models to correct

There is one substitution at a particular position, in divergent sequences

The evolutionary divergence is beyond the ability of the statistical models to correct

The statistical models used to correct homoplasy are called substitution models or evolutionary models

For constructing DNA phylogenies, there are nucleotide substitution models available

Which of the following is incorrect statement about the Kimura model?

It is a model to correct evolutionary distances and is a more sophisticated model

In this, the mutation rates for transitions and transversion are assumed to be different

According to this model, occur more frequently than transversions

According to this model, transversions occur more frequently than transitions

Which of the following is an incorrect statement about Newick Format?

In this linear representation, each internal node is represented by a pair of parentheses

It was designed to provide information of tree topology to computer programs without having to draw the tree itself

In this format, trees are represented by taxa excluded in nested parentheses

In this linear representation, each internal node is represented by a pair of parentheses

For a tree with scaled branch lengths, the branch lengths in arbitrary units are placed immediately after the name of the taxon separated by a colon

The descriptions of morphological traits are often _____ which are due to _____

lucid, more than one genetic factors

ambiguous, multiple genetic factors

lucid, more than one genetic factors

clear, multiple genetic factors

ambiguous, one or two genetic factors

To use molecular data to reconstruct evolutionary history requires making a number of reasonable assumptions. Which of the following is incorrect about it?

Parent branch splits into two daughter branches at any given point

The molecular sequences used in phylogenetic construction are homologous

The molecular sequences used in phylogenetic construction share a common origin

Phylogenetic divergence cannot be bifurcating

Parent branch splits into two daughter branches at any given point

Which of the following is incorrect regarding the advantages of Molecular data for phylogenetics study?

More clear-cut and robust phylogenetic trees can be constructed with the molecular data

They are more numerous than fossil records

They are easier to obtain as compared to fossil records

More clear-cut and robust phylogenetic trees can be constructed with the molecular data

PHYML is a web-based _______ program using the _____

sequence based alignment, GA (Genetic Algorithm )

phylogenetic, GA (Genetic Algorithm )

sequence based alignment, GA (Genetic Algorithm )

phylogenetic, dynamic programming

sequence based alignment, dynamic programming

Which of the following is untrue regarding TREE-PUZZLE?

Because of the heuristic nature of the program, it allows ML analyses of large datasets

It is a program performing quartet puzzling

It allows various substitution models for likelihood score estimation

It doesn‚Äö√Ñ√∂‚àö√ë‚àö¬•t incorporate a discrete ‚âà√≠‚Äö√¢‚Ä¢ model

Because of the heuristic nature of the program, it allows ML analyses of large datasets

101 + Mcqs in Phylogenetic Programs in Bioinformatics Page 2 McqOptions

51.	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.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

52.	MrBayes has a range of probabilistic models available to search for a set of trees with the lowest posterior probability.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

53.	The unweighted method treats all mutations as equivalent.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

57.	Because these ancestral character states are not known directly, multiple possible solutions may exist. In this case, the parsimony principle applies to choose the character states that result in a minimum number of substitutions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

60.	Because there is no indication of which node represents an ancestor, there is no direction of an evolutionary path in an unrooted tree.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

61.	In phylogenetic analysis, it is also important to test whether two competing tree topologies can be distinguished and whether one tree is significantly better than the other.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

64.	For studying the evolution of ________ divergent groups of organisms, one may choose either ______ nucleotide sequences, such as ribosomal RNA or protein sequences.
A.	less widely, slowly evolving
B.	more widely, slowly evolving
C.	more widely, rapidly evolving
D.	less widely, rapidly evolving
Answer» C. more widely, rapidly evolving

65.	A truly robust phylogenetic relationship should have enough characters to support the relationship even if the dataset is perturbed in such away.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

67.	Phylip stands for Phylogenetic inference package (by Joe Felsenstein).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

68.	Molecular clock is an assumption by which molecular sequences evolve at varying rates.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

70.	When the number of taxa exceeds twenty, even the branch-and-bound method becomes computationally unfeasible.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

75.	The maximum likelihood method can be used to explore relationships among more diverse sequences, conditions that are not well handled by maximum parsimony methods.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

76.	The species evolution is the ______ of evolution by _____ in a genome.
A.	combined result, multiple genes
B.	result, single genes
C.	result, sole genes
D.	distinct results, single gene
Answer» B. result, single genes

77.	Evolution of a particular sequence _______ correlate with the evolutionary path of the species.
A.	does not
B.	always
C.	does not necessarily
D.	invariably
Answer» D. invariably

79.	To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

80.	A gene phylogeny only describes the evolution of a particular gene or encoded protein.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

81.	It can be computationally very demanding to find a true phylogenetic tree when the number of sequences is large.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

82.	The number of rooted trees (NR) for n taxa is ______
A.	NR = (2n− 3)!/2ⁿ⁺² (n− 2)!
B.	NR = (2n− 3)!/2ⁿ (n− 2)!
C.	NR = (2n− 3)!/2ⁿ⁻² (n− 5)!
D.	NR = (2n− 3)!/2ⁿ⁻² (n− 2)!
Answer» E.

84.	Sometimes a tree-building method may result in several equally optimal trees. A consensus tree can be built by showing the commonly resolved bifurcating portions and collapsing the ones that disagree among the trees, which results in a polytomy.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

87.	The second step in phylogenetic analysis is to construct sequence alignment. This is probably the most critical step in the procedure because it establishes positional correspondence in evolution.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

89.	Building phylogenetic tree involves bifurcation and multifurcation.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

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.

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

The unweighted method treats all mutations as equivalent.

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

Which of the following is incorrect statement about Maximum Parsimony Method?

Which of the following is incorrect statement about Character-based methods?

Because these ancestral character states are not known directly, multiple possible solutions may exist. In this case, the parsimony principle applies to choose the character states that result in a minimum number of substitutions.

Which of the following is incorrect statement about Building Work of MP tree?

Which of the following is incorrect regarding the terminologies of phylogenetics?

Because there is no indication of which node represents an ancestor, there is no direction of an evolutionary path in an unrooted tree.

In phylogenetic analysis, it is also important to test whether two competing tree topologies can be distinguished and whether one tree is significantly better than the other.

Which of the following is incorrect regarding the terminologies of phylogenetics?

Which of the following is incorrect statement?

For studying the evolution of ________ divergent groups of organisms, one may choose either ______ nucleotide sequences, such as ribosomal RNA or protein sequences.

A truly robust phylogenetic relationship should have enough characters to support the relationship even if the dataset is perturbed in such away.

Which of the following is incorrect regarding the terminologies of phylogenetics?

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

Molecular clock is an assumption by which molecular sequences evolve at varying rates.

Which of the following is untrue regarding TREE-PUZZLE?

When the number of taxa exceeds twenty, even the branch-and-bound method becomes computationally unfeasible.

Which of the following is incorrect about Bootstrapping?

For unrooted trees, the number of unrooted tree topologies (NU) is ________

Which of the following is incorrect statement about Molecular Markers?

Which of the following is untrue about the Fitch–Margoliash?

The maximum likelihood method can be used to explore relationships among more diverse sequences, conditions that are not well handled by maximum parsimony methods.

The species evolution is the ______ of evolution by _____ in a genome.

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

It is often desirable to define the root of a tree. There are two ways to define the root of a tree. One is to use an outgroup, which ______

To obtain a species phylogeny, phylogenetic trees from a variety of gene families need to be constructed.

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

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

The number of rooted trees (NR) for n taxa is ______

Which of the following is incorrect statement about Choosing Substitution Models?

Sometimes a tree-building method may result in several equally optimal trees. A consensus tree can be built by showing the commonly resolved bifurcating portions and collapsing the ones that disagree among the trees, which results in a polytomy.

Which of the following is incorrect statement about the Kimura model?

Which of the following is an incorrect statement about Newick Format?

The second step in phylogenetic analysis is to construct sequence alignment. This is probably the most critical step in the procedure because it establishes positional correspondence in evolution.

The descriptions of morphological traits are often _____ which are due to _____

Building phylogenetic tree involves bifurcation and multifurcation.

Phylogenetics is the study of the evolutionary history of living organisms using treelike diagrams to represent pedigrees of these organisms.

To use molecular data to reconstruct evolutionary history requires making a number of reasonable assumptions. Which of the following is incorrect about it?

Which of the following is incorrect regarding the advantages of Molecular data for phylogenetics study?

MRBAYES_IS_A_BAYESIAN_PHYLOGENETIC_INFERENCE_PROGRAM.?$

MrBayes_has_a_range_of_probabilistic_models_available_to_search_for_a_set_of_trees_with_the_lowest_posterior_probability.$

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

PHYML is a web-based _______ program using the _____

Which of the following is untrue regarding TREE-PUZZLE?

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.

Phylip stands for Phylogenetic inference package (by Joe Felsenstein)

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

For studying the evolution of __ divergent groups of organisms, one may choose either nucleotide sequences, such as ribosomal RNA or protein sequences.

The species evolution is the __ of evolution by _ in a genome.

The descriptions of morphological traits are often _ which are due to _

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

PHYML is a web-based ___ program using the _

95.	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.

100.	In PAUP, The distance options include NJ, ME, FM, and UPGMA.
A.	True
B.	False
Answer» B. False