fdnaml European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnaml http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnaml?wsdl Estimates phylogenies from nucleotide sequences by maximum likelihood. 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/fdnaml.html fdnaml Estimates phylogenies from nucleotide sequences by maximum likelihood. 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/fdnaml.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/fdnaml.html#input.1 http://www.mygrid.org.uk/ontology#nucleotide_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 intreefile_direct_data Type: string. Phylip tree file. This is an optional parameter. No default value available. 'intreefile_direct_data' and 'intreefile_url' are mutually exclusive. String intreefile_url Type: string. URL of Phylip tree file. This is an optional parameter. No default value available.'intreefile_direct_data'and'intreefile_url'are mutually exclusive. String ncategories Type: long. Number of substitution rate categories. This is an optional parameter. 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 lengths Type: boolean(true/false). Use branch lengths from user trees. This is an optional parameter. The default is'false'. false 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 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)| h(User defined HMM of rates)| n(Constant rate). Thedefault is'n'. n 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 ngammacat Type: long. Number of categories. This is an optional parameter. Allowed value: Integer from 1 to 9. The default is 1 1 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 ninvarcat Type: long. Number of categories for invariant sites. This is an optional parameter. Allowed value: Integer between 1-9. The default is 1 1 String invarfrac Type: float. Fraction of invariant sites. This is an optional parameter. The default is 0.0 0.0 String nhmmcategories Type: long. Number of HMM rate categories. This is an optional parameter. Allowed value: Integer between 1-9. The default is 1 1 String hmmrates Type: float. HMM category rates. This is an optional parameter. The default is 1.0 1.0 String hmmprobabilities Type: float. Probability for each HMM category. This is an optional parameter. The default is 1.0 1.0 String adjsite Type: boolean(true/false). Rates at adjacent sites correlated. This is an optional parameter. The default is'false'. false String lambda Type: float. Mean block length of sites having the same rate. This is an optional parameter. The default is 1.0 1.0 String njumble Type: long. Number of times to randomise. This is an optional parameter. The default is 0 0 String seed Type: long. Random number seed between 1 and 32767 (must be odd). This is an optional parameter. The default is 1. 1 String global Type: boolean(true/false). Global rearrangements. This is an optional parameter. The default is'false'. false String outgrno Type: long. Species number to use as outgroup. This is an optional parameter. The default is 0 0 String rough Type: boolean(true/false). Speedier but rougher analysis. This is an optional parameter. The default is'true'. true String trout Type: boolean (Yes/No). Write out trees to tree file. This is an optional parameter. The default is'Yes'. Y 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 treeprint Type: boolean(true/false). Print out tree. This is an optional parameter. The default is'true'. true String hypstate Type: boolean(true/false). Reconstruct hypothetical sequence. This is an optional parameter. The default is'false' false 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 phylogenetic tree from nucleotide sequences by maximum likelihood. The output starts by giving the number of species, the number of sites, and the base frequencies for A, C, G, and T that have been specified. It then prints out the transition/transversion ratio that was specified or used by default. http://www.mygrid.org.uk/ontology#phylogenetic_tree String outtreefile Returns phylogenetic tree file. String http://www.mygrid.org.uk/ontology#predicting http://www.mygrid.org.uk/ontology#nucleotide_sequence_database http://www.mygrid.org.uk/ontology#phylogenetic_algorithm Soaplab service