fdnapenny European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnapenny http://www.ebi.ac.uk/soaplab/emboss4/services/phylogeny_molecular_sequence.fdnapenny?wsdl Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10-11 species or so. 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/fdnapenny.html fdnapenny Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10-11 species or so. 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/fdnapenny.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 beembl, 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.ssprot 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 hasn't 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/fdnapenny.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 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 howoften Type: long. How often to report, in trees. This is an optional parameter. The default is 100 100 String howmany Type: long. How many groups of trees. This is an optional parameter. The default is 1000 1000 String simple Type: boolean(true/false). Branch and bound is simple. This is an optional parameter. The default is'true' true String outgrno Type: long. Species number to use as outgroup. This is an optional parameter. The default is 0 0 String thresh Type: boolean(Yes/No). Use threshold parsimony. This is an optional parameter. The default is'No' N String threshold Type: float. Threshold value. This is an optional parameter. The default is 1.0 1.0 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). Printout tree. This is an optional parameter. The default is'true'. true String stepbox Type: boolean(true/false). Print out steps in each site. This is an optional parameter. The default is'false' false String ancseq Type: boolean(true/false). Print sequences at all nodes of tree. 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 all most parsimonious phylogenetic trees for nucleic acid sequences by branch-and-bound search. 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