ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It attempts to calculate the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Input parameters for the tool Alignment Method [The alignment method used to perform the pairwise alignments used to generate the guide tree.] Sequence type [Indicates if the sequences to align are protein or nucleotide (DNA/RNA).] KTUP [Fast pairwise alignment word size used to find matches between the sequences. Decrease for sensitivity; increase for speed.] Window [Fast pairwise alignment window size for joining word matches. Decrease for speed; increase for sensitivity.] Score [Fast pairwise alignment score type to output.] Top Diagonals [Fast pairwise alignment number of match regions are used to create the pairwise alignment. Decrease for speed; increase for sensitivity.] Pairgap [Fast pairwise alignment gap penalty for each gap created.] Protein Weight Matrix [Slow pairwise alignment protein sequence comparison matrix series used to score alignment.] DNA Weight Matrix [Slow pairwise alignment nucleotide sequence comparison matrix used to score alignment.] Gap open [Slow pairwise alignment score for the first residue in a gap.] Gap extend [Slow pairwise alignment score for each additional residue in a gap.] Protein Weight Matrix [Multiple alignment protein sequence comparison matrix series used to score the alignment.] DNA Weight Matrix [Multiple alignment nucleotide sequence comparison matrix used to score the alignment.] Gap open [Multiple alignment penalty for the first residue in a gap.] End gap [Multiple alignment disable the gap seperation penalty when scoring gaps the the ends of the alignment] Gap extend [Multiple alignment penalty for each additional residue in a gap.] Gap distance [Multiple alignment gaps that are closer together than this distance are penalised.] Iteration type [Multiple alignment improvement iteration type] Number Iterations [Maximum number of iterations to perform] Clustering [Clustering type.] Alignment format [Format for generated multiple sequence alignment.] Output order [The order in which the sequences appear in the final alignment] Sequence [Three or more sequences to be aligned can be entered directly into this form. Sequences can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format, and if protein secondary structure information is available in the input it will be used to guide the alignment. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.] List of renderers available to output the result of the job Details about a renderer used to output the result of the job A short description of the renderer A suggested file suffix to be used when saving the data formatted by the renderer The renderer identifier to be used when invoking the getResult() method A more appropriate name for the renderer (more meaningful than the identifier) The media type (MIME) of the renderer's output A set of parameters passed to a renderer when formatting the data A parameter used by the renderer The name of the parameter The parameter value as an array of String List the names of the tool parameters Details about a tool parameter The name of the parameter A short description of the parameter The type of the parameter The list of values available for this parameter The list of parameter values The details about a parameter values A meaningful label for the parameter value The real value A flag indicating whether this value is a default value or not A set of additional properties associated with the parameter value A set of properties A key/value pair association of information User email address A title to identify the analysis job The list of parameters to be used for launching the analysis A unique identifier for the analysis job An identifier for the job to check The status of the job (FINISHED, ERROR, RUNNING, NOT_FOUND or FAILURE) An identifier for the job to check The list of renderers available An identifier for the job to check The renderer to be used to format the output A list of parameters to be passed on to the renderer The identifier for the parameter The parameter details The list of parameter available for this tool Submit an analysis job Get the status of a submitted job Get the list of renderers available to output a job result (i.e. the list of available output types) Get a job result formatted using a particular renderer List the names of the parameters available before submission Get some details about a parameter (e.g. name, description, values, etc.) Submit an analysis job Get the status of a submitted job Get the list of renderers available to output a job result (i.e. the list of available output types) Get a job result formatted using a particular renderer List the names of the parameters available before submission Get some details about a parameter (e.g. name, description, values, etc.)