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ClustalW FAQ (Frequently Asked Questions)
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What
is the difference between a guide tree and a true phylogenetic tree?
A guide tree is calculated based on the distance matrix
that is generated from the pairwise scores. The output can be found in the .dnd
file. A phylogenetic tree is calculated based on the multiple alignment that it
receives. The distances between the sequences in the alignment are calculated
and can be found in the .ph file. These distances are then used by the method
chosen (nj, phylip, dist) to make the phylogenetic tree (.nj, .ph, .dst file).
Where can I find detailed
information about ClustalW?
There are a number of places:
For additional help on ClustalW also see:
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.
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.
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.
3. Combine the alignments, starting from the closest related groups
(going form the tips of the tree towards the root).
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