CLUSTALW, Phylogenetic Analysis, Guide Tree, Dendrogram, NSYS, UPGMA, Morphological, Molecular

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CLUSTALW.

This is a programme for progressive multiple sequence alignment. The principle used in this programme is used for phylogenetic analysis, and involves the following steps: (i) A a pair-wise distance matri for all the sequences to be aligned is generated and a guide tree is created using the neighbour-joining algorithm. (ii) Each of the most closely related pairs of sequences in the ultimate branches of the guide tree are aligned to each other. (iii) The less related sequences are then aligned to build a profile. Finally profiles are aligned to each other until a full dendrogram is obtained. This programme is similar to programmes like NSYS, UPGMA, which make use of morphological or molecular marker data for preparation of distance matrix and the dendrogram, except that it utilizes DNA or protein sequences.

CLUSTALW can also be used for pairwise global protein or nucleic acid sequence alignments between ORFs having a significant BLAST alignment (E <10-10). This will give the level of divergence for each of the large number of pairwise comparisons, which can be used for comparative genomics research.

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