Question

1-Describe the differences between genome assemblers that utilise a greedy algorithm versus de Bruijn graphs.

2-Describe the different approaches that are undertaken when reconstructing a phylogenetic species supertree. In your answer, discuss why it is beneficial to have a robust tree of life.

Please answer these 2 questions, Thank you

Answer 1

1. A de Bruijn graph can be constructed for any sequence which is short or long. An n-dimensionalof m symbols is a directed graph representing overlaps between sequences of symbols. It has mⁿ vertices, comprises of all possible length-n sequences of the given symbols where as greedy algorithms find overlap between all reads, use the overlap to determine a layout or tiling of the reads, and then produce a consensus sequence.

2. Different approaches inclue labelled or unlabelled, biurcating,multiurcating enumerating,rooted and unrooted with types including dendrogram,cladogram,chronogram,dahlgrenogram etc.
Lasso approach is most common, distance-based and rendering it very fast to run and suitable for data sets of all sizes, including large data sets such as those generated by modern Next Generation Sequencing technologie which means for reconstructing rooted phylogenetic trees from distance matrices with missing values.
Robust phylogenomic approach is to infer evolutionary relationships among genomes that span the diversity of species to identify conflicts in the phylogeny,and to determine the likely underlying factors of the observed conflicts.