Bioinformatics Mcqs

Page No. 59

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.


aTrue

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b False

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ceither true and false

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dnone of these

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View Answer True

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


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

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

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

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dFor 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

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

. 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.


aTrue

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bFalse

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ceither true and false

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dnone of these

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View Answer True

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


a 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

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b It starts by randomly clustering two taxa in a node

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cIt starts by creating three equations to describe the distances

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dThe method searches for some specific tree topologi

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View Answer The method searches for some specific tree topologi

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


aThe clustering-based methods produce multiple trees as output

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

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

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

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View Answer The clustering-based methods produce multiple trees as output

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


a True

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b False

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ceither true and false

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dnone of these

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View Answer False

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


ari = ∑dij + dj2

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b ri = ∑dij

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c ri = ∑dij + di

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d ri = ∑dij + dj

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View Answer ri = ∑dij

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 ______


a dAB’ = dAB − 1/4 × (rA + rB)

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bdAB’ = dAB − 1/2 × (rA + rB)

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cdAB’ = dAB − 1/3 × (rA + rB)

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ddAB’ = (dAB/3) − 1/2 × (rA + rB)

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View Answer dAB’ = dAB − 1/2 × (rA + rB)

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


a True

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b False

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ceither true ad false

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dnone of these

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View Answer True

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.


aTrue

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bFalse

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ceither true and false

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dnone of these

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View Answer True

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