fprotdist European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fprotdist http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fprotdist?wsdl Computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. Detailed info about this operation can be found at the following link: http://genome.jouy.inra.fr/doc/genome/suite-logicielle/emboss/html/embassy/phylipnew/fprotdist.html fprotdist Computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. Detailed info about this operation can be found at the following link: http://genome.jouy.inra.fr/doc/genome/suite-logicielle/emboss/html/embassy/phylipnew/fprotdist.html sequence_usa Type: string. File containing one or more protein sequence aligment. The Uniform Sequence Address, or USA, is a standard way of specifying a sequence to be read into a program in EMBOSS. The most common ways of specifying a sequence is to type (database:entry), where database can be embl, uniprot or swissprot and entry is either the sequence`s entry or ID name, or its Accession number in that database. For example:database:accession -->embl:X65923 or swissprot:Q7M4G0 | database:entry_name -->swissprot:AMIC_PSEAE |database:ID_name -->embl:paamir.Choose either this parameter or the sequence_direct_data parameter but not both together. Parameter mandatory if the sequence_direct_data parameter has not been chosen. String sequence_direct_data Type: string. File containing one or more protein sequence alignment. Choose this parameter if you want to provide the'sequence'value as string. Parameter mandatory if the sequence_usa parameter hasn't been chosen. An example input can be found here: http://genome.jouy.inra.fr/doc/genome/suite-logicielle/emboss/html/embassy/phylipnew/fprotdist.html#input.1 http://www.mygrid.org.uk/ontology#protein_sequence String sformat Type: string. Specifies the format of the input sequence. This is an optional parameter. The allowed values for this parameter are: gcg, gcg8, embl, swiss, fasta, ncbi, genbank, nbrf, pir, codata, strider, clustal, phylip, acedb, msf, jackknifer, jackknifernon, nexus, nexusnon, treecon, mega, meganon, ig, staden, text, raw. String sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 (default value) means start with the first base in the sequence. This is an optional parameter. String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end of the sequence. String sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. String snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. String ncategories Type: long. Number of substitution rate categories. This is an optional parameter. Allowed values: Integer from 1 to 9. The default is 1. 1 String rate Type: string. Rate for each category. This is an optional parameter. String categories_direct_data Type: string. File of substitution rate categories. This is an optional parameter. No default value available String categories_url Type: string. URL of file of substitution rate categories. This is an optional parameter.'categories_url'and'categories_direct_data'are mutually exclusive. String weights_direct_data Type: string. Phylip weights file. This is an optional parameter. No default value available.'weights_direct_data'and'weights_url'are mutually exclusive. String weights_url Type: string. URL of Phylip weights file.This is an optional parameter. No default value available.'weights_direct_data'and'weights_url'are mutually exclusive. String method Type: string. Method to use. This is an optional parameter. The allowed values for this parameter are: j(Jones-Taylor-Thornton matrix)| h(Henikoff/Tiller PMB matrix) | d(Dayhoff PAM matrix)| k(Kimura formula)| s(Similarity table)| c(Categories model). The default is 'j'. j String gamma Type: string. Rate variation among sites. This is an optional parameter. The allowed values for this parameter are: g(Gamma distributed rates)| i(Gamma+invariant sites)| c(Constant rate). The default is 'c'. c String gammacoefficient Type: float. Coefficient of variation of substitution rate among sites. This is an optional parameter. The default is 1.0 1.0 String invarcoefficient Type: float. Coefficient of variation of substitution rate among sites. This is an optional parameter. The default is 1.0 1.0 String aacateg Type: string. Which categorizations of amino acids to use. This is an optional parameter. The allowed values for this parameter are: G(George/Hunt/Barker (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr Pro))| C(Chemical (Cys Met), (Val Leu Ileu Gly Ala Ser Thr), (Pro))| H(Hall (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr),(Pro)). The default is 'G' G String whichcode Type: string. Which genetic code to use. This is an optional parameter. The allowed values for this parameter are: u(Universal)| c(Ciliate)| m(Universal mitochondrial)| v(Vertebrate mitochondrial)| f(Fly mitochondrial)| y(Yeast mitochondrial). The default is 'u' u String ease Type: float. Probability change category (1.0=easy).This is an optional parameter. Allowed values: Number between 0.00-1.00. The default is 0.457 0.457 String ttratio Type: float. Transition/transversion ratio. This is an optional parameter. The default is 2.0 2.0 String basefreq Type: float. Base frequencies for A C G T/U (use blanks to separate). This is an optional parameter. The default is 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 String printdata Type: boolean(True/False). Print data at start of run. This is an optional parameter. The default is'false' false String progress Type: boolean(True/False). Print indications of progress of run. This is an optional parameter. The default is'True'. true String report Type: string. A general report for the underlying analysis job. String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. String outfile Returns distances between species from protein sequences. fprodist output contains on its first line the number of species. The distance matrix is then printed in standard form, with each species starting on a new line with the species name, followed by the distances to the species in order. In general the format of the distance matrix is such that it can serve as input to any of the distance matrix programs. String http://www.mygrid.org.uk/ontology#calculating Soaplab service