Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. Input parameters for the tool Output guide tree [Output guide tree.] Output distance matrix [Output distance matrix. This is only calculated if the mBed-like clustering guide tree is set to false.] Dealign input sequences [Remove any existing alignment (gaps) from input sequences.] mBed-like clustering guide tree [This option uses a sample of the input sequences and then represents all sequences as vectors to these sequences, enabling much more rapid generation of the guide tree, especially when the number of sequences is large.] mBed-like clustering iteration [Use mBed-like clustering during subsequent iterations.] Number of iterations [Number of (combined guide-tree/HMM) iterations.] Maximum guide tree iterations [Having set the number of combined iterations, this parameter can be changed to limit the number of guide tree iterations within the combined iterations.] Maximum HMM iterations [Having set the number of combined iterations, this parameter can be changed to limit the number of HMM iterations within the combined iterations.] Output alignment format [Format for generated multiple sequence alignment.] Sequence Type [Defines the type of the sequences to be aligned] Sequence [Three or more sequences to be aligned can be entered directly into this box. Sequences can be be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. 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. There is currently a limit of 2000 sequences and 2MB of data.] 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 Base64 encoded data corresponding to the output of the job formatted by 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.)