What is LMS?
LMS stands for Local Matching Score. CLAP incorporates LMS to generate pairwise distances between a set of amino acid sequences. The details of the method have been given in the Help section.
What is a distance cut-off?
Using a particular clustering method, a distance matrix can be converted to a dendrogram. This helps to visually observe the similarities and differences in the data set being studied. Thus, the height of a phylogenetic tree or a particular clade is representative of the dissimilarity between the nodes. When the final tree is parsed at a particular height, this height is the distance cut-off being used to generate separate clusters.
How is the tree generated?
Ward's minimum variance method as implemented in R statistical package is employed to cluster the sequences.For detail please refer to Help section.
Is it necessary to give a distance cut-off?
Only if a distance cut-off is input, can the dendrogram be parsed and clusters obtained. It is not required in case the user wants to study only the phylogenetic relationship between the sequences. Also, if the user wants to compute domain architecture similarities of each cluster then the cut-off should be provided.
How to select the distance cut-off?
Parsing the tree at different cut-offs will generate different clustering patterns. Hence, the best cut-off will be the one which maximizes inter-cluster and minimizes intra-cluster dissimilarities. Several indices like dunn index, Hubert-gamma index can be used to determine the optimal cut-off. This feature is not currently a part of CLAP, but will soon be incorporated in the server.
What does Results(.tar format) contain?
The Results.tar file is provided only if the user specifies a particular distance cut-off. Else the link is not operative. Following output files are present in Results.tar - Readme.txt, Input.fasta, Dist.txt, tree.nwk, scaled_tree.nwk, Clusters_x.txt, and colored_dendrogram.png. The description for each file is listed in the Readme.txt file. In case the user inputs an email-id, a dynamic link will alsobe to mailed that address.
The server shows an error?
If there is a SOFTWARE ERROR saying 'MSG: Could not open scaled_tree.nwk: No such file or directory', please remove any blank lines from your input fasta file and re-run CLAP.