fproml European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fproml http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fproml?wsdl Estimates phylogenies from protein amino acid 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/fproml.html fproml Estimates phylogenies from protein amino acid 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/fproml.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. 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/fproml.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 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 model Type: string. Probability model for amino acid change. This is an optional parameter. The allowed values for this parameter are: j(Jones-Taylor-Thornton)| h(Henikoff/Tillier PMBs)| d(Dayhoff PAM). 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)| h(User defined HMM of rates)| n(Constant rate). The default 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 between 1-9. 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: string. 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, choose 0 if you don't want 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. No simpleParameter String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. No simpleParameter String outfile Returns phylogenetic tree from protein sequences by maximum likelihood. 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#phylogenetic_algorithm Soaplab service