Question

Which of the following is incorrect about nonparametric bootstrapping?

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

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

(c) Certain sites are randomly replaced by other existing sites

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

The question was asked by my school principal while I was bunking the class.

Query is from Phylogenetic Tree Evaluation topic in portion Phylogenetic Tree Construction Methods and Programs of Bioinformatics

Answer 1

Correct option is (b) A new multiple sequence alignment of the distinct lengths is generated with random duplication of some of the sites

Best explanation: In nonparametric bootstrapping, a new multiple sequence alignment of the same length is generated with random duplication of some of the sites (i.e., the columns in an alignment) at the expense of some other sites. This process is repeated 100 to 1,000 times to create 100 to 1,000 new alignments that are used to reconstruct phylogenetic trees using the same method as the originally inferred tree.