fdnadist European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnadist http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnadist?wsdl Nucleic acid sequence Distance Matrix program. Computes four different distances between species from nucleic acid sequences. 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/fdnadist.html fdnadist Nucleic acid sequence Distance Matrix program. Computes four different distances between species from nucleic acid sequences. 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/fdnadist.html sequence_usa Type: string. File containing one or more 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 sequence. 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/fdnadist.html#input.1 http://www.mygrid.org.uk/ontology#nucleotide_sequence http://www.mygrid.org.uk/ontology#single_sequence_format 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 method Type: string. Distance methods to use. This is an optional parameter. The allowed values for this parameter are: f(F84 distance model)| k (Kimura 2-parameter distance)| j(Jukes-Cantor distance)| l(LogDet distance)| s(Similarity table).The default is'f' f String gamma Type: string. Gamma distribution to use. This is an optional parameter. The allowed values for this parameter are: g(Gamma distributed rates)| i(Gamma+invariant sites)| n(No distribution parameters used).The default is'n' n 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: float. Category rates. This is an optional parameter. The default is 1.0 1.0 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 gammacoefficient Type: float. Coefficient of variation of substitution rate among sites. This is an optional parameter. The default is 1.0 1.0 String invarfrac Type: float. Fraction of invariant sites. This is an optional parameter. The default is 0.0 0.0 String ttratio Type: float. Transition/transversion ratio. This is an optional parameter. The default is 2.0 2.0 String freqsfrom Type: boolean(Yes/No). Use empirical base frequencies from seqeunce input. This is an optional parameter. The default is'Yes'. Y 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 lower Type: boolean(true/false). Lower triangular distance matrix. This is an optional parameter. The default is'false' false 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 nucleic acid sequences. fdnadist 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 http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service