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About Soaplab
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- Soaplab overview
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Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
UNITED KINGDOM
Submitter/Source:
Mike Mayer (over 9 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/phylogeny_molecular_sequence.distmat
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/phylogeny_molecular_sequence.distmat?wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): No description(s) yet Login to add a description ELIXIR Description(s): No info yet Login to add an elixir description Details (from Soaplab server): from Soaplab server(over 8 years ago)
- ds_lsr_analysis :
- analysis :
- name : distmat
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Phylogeny Molecular sequence
- description : Create a distance matrix from a multiple sequence alignment
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : distmat
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Phylogeny Molecular sequence
- description : Create a distance matrix from a multiple sequence alignment
- analysis_extension :
- parameter :
- data :
- list :
- list_item :
- level : 0
- value : abi
- level : 0
- value : ace
- level : 0
- value : acedb
- level : 0
- value : bam
- level : 0
- value : biomart
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : dbid
- level : 0
- value : embl
- level : 0
- value : ensembl
- level : 0
- value : experiment
- level : 0
- value : fasta
- level : 0
- value : fastq
- level : 0
- value : fastq-illumina
- level : 0
- value : fastq-sanger
- level : 0
- value : fastq-solexa
- level : 0
- value : fitch
- level : 0
- value : gcg
- level : 0
- value : genbank
- level : 0
- value : genpept
- level : 0
- value : gff2
- level : 0
- value : gff3
- level : 0
- value : gifasta
- level : 0
- value : hennig86
- level : 0
- value : ig
- level : 0
- value : igstrict
- level : 0
- value : jackknifer
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : nexus
- level : 0
- value : pdb
- level : 0
- value : pdbnuc
- level : 0
- value : pdbnucseq
- level : 0
- value : pdbseq
- level : 0
- value : pearson
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : raw
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : stockholm
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- list_item :
- list :
- base :
- data :
- result :
- iotype : output
- base :
- standard :
- list :
- list_item :
- shown_as : Uncorrected
- level : 0
- value : 0
- shown_as : Jukes-Cantor
- level : 0
- value : 1
- shown_as : Kimura
- level : 0
- value : 2
- shown_as : Tamura
- level : 0
- value : 3
- shown_as : Tajima-Nei
- level : 0
- value : 4
- shown_as : Jin-Nei Gamma
- level : 0
- value : 5
- name : Multiple substitution correction methods for nucleotides
- type : full
- list_item :
- repeatable :
- list :
- base :
- standard :
- list :
- list_item :
- shown_as : Uncorrected
- level : 0
- value : 0
- shown_as : Jukes-Cantor
- level : 0
- value : 1
- shown_as : Kimura Protein
- level : 0
- value : 2
- name : Multiple substitution correction methods for proteins
- type : full
- list_item :
- repeatable :
- list :
- base :
- base :
- name : ambiguous
- ordering : 8
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins.
- default : false
- qualifier : ambiguous
- mandatory : false
- prompt : Use the ambiguous codes in the calculation.
- type : boolean
- range :
- format : %f
- repeatable :
- base :
- name : gapweight
- ordering : 9
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- help : Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods.
- default : 0.
- qualifier : gapweight
- mandatory : false
- prompt : Weight given to gaps
- type : float
- range :
- format : %d
- repeatable :
- base :
- name : position
- ordering : 10
- option :
- name : EDAM:0001016
- type : normal
- value : data Sequence position
- help : Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases.
- default : 123
- qualifier : position
- mandatory : false
- prompt : Base position to analyse
- type : long
- base :
- name : calculatea
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This will force the calculation of parameter ‘a’ in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option).
- default : false
- qualifier : calculatea
- mandatory : false
- prompt : Calculate the nucleotide Jin-Nei parameter ‘a’
- type : boolean
- range :
- format : %f
- repeatable :
- base :
- name : parametera
- ordering : 12
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- help : User defined parameter ‘a’ to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 (Jin et al.) and this is the default.
- default : 1.0
- qualifier : parametera
- mandatory : false
- prompt : Nucleotide Jin-Nei parameter ‘a’
- type : float
- data :
- option :
- name : EDAM:0000084
- type : normal
- value : topic Phylogenetics
- name : EDAM:0000159
- type : normal
- value : topic Sequence comparison
- name : EDAM:0000289
- type : normal
- value : operation Sequence distance matrix generation
- name : emboss
- type : normal
- value : true
- name : installation
- type : normal
- value : Soaplab2 default installation
- name : version
- type : normal
- value : 6.3.0
- app_info :
- category : phylogeny_molecular_sequence
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/distmat.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : ambiguous
- default : false
- mandatory : false
- type : boolean
- name : gapweight
- default : 0.
- mandatory : false
- type : float
- name : position
- default : 123
- mandatory : false
- type : long
- name : calculatea
- default : false
- mandatory : false
- type : boolean
- name : parametera
- default : 1.0
- mandatory : false
- type : float
- analysis :
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