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(Continued from previous question...)
How does Clustalw Work (very simple explanation)?
1. Determine all pairwise alignments between sequences and the degree of
similarity between them:
2. Construct a similarity tree.
3. Combine the alignments from 1 in the order specified in 2 using the
rule " once a gap always a gap"
In stage 1:
1.1. clustalw uses a pairwise alignment to compute pairwise alignments.
2. Using the matrix from 1.2.1. and Neighbor-Joining, Clustalw
constructs the similarity tree. The root is placed in the middle
of the longest chain of consecutive edges.
1.2. Using the alignments from 1.1 it computes a distance.
1.2.1. The distance is commonly calculated by looking at the non-gapped
positions and count the number of mistmatches between the two sequences.
Then divide this value by the number of non-gapped pairs to calculate
the distance. Once all
distances for all pairs are calculated they go into a matrix. This
follows on in stage 2.
3. Combine the alignments, starting from the closest related groups
(going form the tips of the tree towards the root).