Information on a multiple sequence alignment qualifiers for parameter: sequence Similarity scoring Matrix file This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. The number or the name of the reference sequence If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. Plurality check % for consensus Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. Required % of identities at a position fro consensus Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. Format output as an HTML table Format output as an HTML table Display the specified columns This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight' to get only the sequence length output, you can specify '-only -seqlength' Display column headings Display column headings Display the USA of the sequence Display the USA of the sequence Display 'name' column Display 'name' column Display 'seqlength' column Display 'seqlength' column Display 'alignlength' column Display 'alignlength' column Display number of gaps Display number of gaps Display number of gap positions Display number of gap positions Display number of identical positions Display number of identical positions Display number of similar positions Display number of similar positions Display number of different positions Display number of different positions Display % number of changed positions Display % number of changed positions Display 'weight' column Display 'weight' column Display 'description' column Display 'description' column Display 'description' column Display 'description' column Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id) Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id)