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About Soaplab
Soaplab services are command line applications, wrapped as SOAP services, and served from a Soaplab server. All Soaplab services have the same generic set of SOAP operations (depending on the Soaplab version) as they all share a standardised interface.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
More information on Soaplab clients is available here.
Further documentation on Soaplab services is available:
- Soaplab overview
- Soaplab client guide page
- EBI Soaplab server documentation
- Soaplab 2
- Sourceforge site for EMBOSS Soaplab services
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/alignment_multiple.emma
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/alignment_multiple.emma?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(about 8 years ago)
- ds_lsr_analysis :
- analysis :
- name : emma
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Multiple
- description : Multiple sequence alignment (ClustalW wrapper)
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : emma
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Multiple
- description : Multiple sequence alignment (ClustalW wrapper)
- 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 :
- extension : dnd
- iotype : output
- base :
- base :
- name : onlydend
- ordering : 3
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : onlydend
- mandatory : false
- prompt : Only produce dendrogram file
- type : boolean
- base :
- name : dend
- ordering : 4
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : dend
- mandatory : false
- prompt : Do alignment using an old dendrogram
- type : boolean
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- base :
- name : slow
- ordering : 6
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : A distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment. The scores are calculated from separate pairwise alignments. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate). The slow-accurate method is fine for short sequences but will be VERY SLOW for many (e.g. >100) long (e.g. >1000 residue) sequences.
- default : false
- qualifier : slow
- mandatory : false
- prompt : Do you want to carry out slow pairwise alignment
- type : boolean
- standard :
- list :
- list_item :
- shown_as : blosum
- level : 0
- value : b
- shown_as : pam
- level : 0
- value : p
- shown_as : gonnet
- level : 0
- value : g
- shown_as : id
- level : 0
- value : i
- shown_as : own
- level : 0
- value : o
- name : Protein pairwise alignment matrix options
- type : full
- list_item :
- repeatable :
- list :
- base :
- standard :
- list :
- list_item :
- shown_as : iub
- level : 0
- value : i
- shown_as : clustalw
- level : 0
- value : c
- shown_as : own
- level : 0
- value : o
- name : DNA pairwise alignment matrix options
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- standard :
- list :
- list_item :
- shown_as : blosum
- level : 0
- value : b
- shown_as : pam
- level : 0
- value : p
- shown_as : gonnet
- level : 0
- value : g
- shown_as : id
- level : 0
- value : i
- shown_as : own
- level : 0
- value : o
- name : Protein multiple alignment matrix options
- type : full
- list_item :
- repeatable :
- list :
- base :
- standard :
- list :
- list_item :
- shown_as : iub
- level : 0
- value : i
- shown_as : clustalw
- level : 0
- value : c
- shown_as : own
- level : 0
- value : o
- name : Nucleotide multiple alignment matrix options
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- min : 0.0
- repeatable :
- base :
- name : pwgapopen
- ordering : 20
- option :
- name : EDAM:0001397
- type : normal
- value : data Gap opening penalty
- name : scalemin
- type : style
- value : 0.0
- help : The penalty for opening a gap in the pairwise alignments.
- default : 10.0
- qualifier : pwgapopen
- mandatory : false
- prompt : Slow pairwise alignment: gap opening penalty
- type : float
- range :
- format : %f
- min : 0.0
- repeatable :
- base :
- name : pwgapextend
- ordering : 21
- option :
- name : EDAM:0001398
- type : normal
- value : data Gap extension penalty
- name : scalemin
- type : style
- value : 0.0
- help : The penalty for extending a gap by 1 residue in the pairwise alignments.
- default : 0.1
- qualifier : pwgapextend
- mandatory : false
- prompt : Slow pairwise alignment: gap extension penalty
- type : float
- range :
- format : %d
- max : 4
- min : 0
- repeatable :
- base :
- name : ktup
- ordering : 24
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : calculated_default
- type : normal
- value : ${acdprotein}?1:2
- name : scalemax
- type : style
- value : 4
- help : This is the size of exactly matching fragment that is used. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity. For longer sequences (e.g. >1000 residues) you may need to increase the default.
- qualifier : ktup
- mandatory : false
- prompt : Fast pairwise alignment: similarity scores: K-Tuple size
- type : long
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : gapw
- ordering : 25
- option :
- name : EDAM:0002137
- type : normal
- value : data Gap penalty
- name : calculated_default
- type : normal
- value : ${acdprotein}?3:5
- help : This is a penalty for each gap in the fast alignments. It has little affect on the speed or sensitivity except for extreme values.
- qualifier : gapw
- mandatory : false
- prompt : Fast pairwise alignment: similarity scores: gap penalty
- type : long
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : topdiags
- ordering : 26
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : calculated_default
- type : normal
- value : ${acdprotein}?5:4
- help : The number of k-tuple matches on each diagonal (in an imaginary dot-matrix plot) is calculated. Only the best ones (with most matches) are used in the alignment. This parameter specifies how many. Decrease for speed; increase for sensitivity.
- qualifier : topdiags
- mandatory : false
- prompt : Fast pairwise alignment: similarity scores: number of diagonals to be considered
- type : long
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : window
- ordering : 27
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : calculated_default
- type : normal
- value : ${acdprotein}?5:4
- help : This is the number of diagonals around each of the ‘best’ diagonals that will be used. Decrease for speed; increase for sensitivity.
- qualifier : window
- mandatory : false
- prompt : Fast pairwise alignment: similarity scores: diagonal window size
- type : long
- base :
- name : nopercent
- ordering : 28
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : nopercent
- mandatory : false
- prompt : Fast pairwise alignment: similarity scores: suppresses percentage score
- type : boolean
- range :
- format : %f
- min : 0.0
- repeatable :
- base :
- name : gapopen
- ordering : 31
- option :
- name : EDAM:0001397
- type : normal
- value : data Gap opening penalty
- name : scalemin
- type : style
- value : 0.0
- help : The penalty for opening a gap in the alignment. Increasing the gap opening penalty will make gaps less frequent.
- default : 10.0
- qualifier : gapopen
- mandatory : false
- prompt : Multiple alignment: Gap opening penalty
- type : float
- range :
- format : %f
- min : 0.0
- repeatable :
- base :
- name : gapextend
- ordering : 32
- option :
- name : EDAM:0001398
- type : normal
- value : data Gap extension penalty
- name : scalemin
- type : style
- value : 0.0
- help : The penalty for extending a gap by 1 residue. Increasing the gap extension penalty will make gaps shorter. Terminal gaps are not penalised.
- default : 5.0
- qualifier : gapextend
- mandatory : false
- prompt : Multiple alignment: Gap extension penalty
- type : float
- base :
- name : endgaps
- ordering : 33
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : End gap separation: treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by ‘gap separation distance’). If you turn this off, end gaps will be ignored for this purpose. This is useful when you wish to align fragments where the end gaps are not biologically meaningful.
- default : false
- qualifier : endgaps
- mandatory : false
- prompt : Use end gap separation penalty
- type : boolean
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : gapdist
- ordering : 34
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- help : Gap separation distance: tries to decrease the chances of gaps being too close to each other. Gaps that are less than this distance apart are penalised more than other gaps. This does not prevent close gaps; it makes them less frequent, promoting a block-like appearance of the alignment.
- default : 8
- qualifier : gapdist
- mandatory : false
- prompt : Gap separation distance
- type : long
- base :
- name : norgap
- ordering : 35
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Residue specific penalties: amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence. As an example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine.
- default : false
- qualifier : norgap
- mandatory : false
- prompt : No residue specific gaps
- type : boolean
- standard :
- repeatable :
- base :
- base :
- name : nohgap
- ordering : 37
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Hydrophilic gap penalties: used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common. The residues that are ‘considered’ to be hydrophilic are set by ‘-hgapres’.
- default : false
- qualifier : nohgap
- mandatory : false
- prompt : No hydrophilic gaps
- type : boolean
- range :
- format : %d
- max : 100
- min : 0
- repeatable :
- base :
- name : maxdiv
- ordering : 39
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : scalemax
- type : style
- value : 100
- help : This switch, delays the alignment of the most distantly related sequences until after the most closely related sequences have been aligned. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level to any other sequences will be aligned later.
- default : 30
- qualifier : maxdiv
- mandatory : false
- prompt : Cut-off to delay the alignment of the most divergent sequences
- type : long
- data :
- result :
- extension : aln
- iotype : output
- base :
- standard :
- list :
- list_item :
- level : 0
- value : acedb
- level : 0
- value : asn1
- level : 0
- value : bam
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : das
- level : 0
- value : dasdna
- level : 0
- value : embl
- level : 0
- value : experiment
- level : 0
- value : fasta
- 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 : jackknifer
- level : 0
- value : jackknifernon
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : meganon
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : ncbi
- level : 0
- value : nexus
- level : 0
- value : nexusnon
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : pir
- level : 0
- value : raw
- level : 0
- value : refseq
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- option :
- name : EDAM:0000186
- type : normal
- value : topic Multiple sequence alignment
- name : EDAM:0000499
- type : normal
- value : operation Phylogenetic tree-based multiple sequence alignment
- 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 : alignment_multiple
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/emma.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : onlydend
- default : false
- mandatory : false
- type : boolean
- name : dend
- default : false
- mandatory : false
- type : boolean
- name : slow
- default : false
- mandatory : false
- type : boolean
- name : pwgapopen
- default : 10.0
- mandatory : false
- type : float
- name : pwgapextend
- default : 0.1
- mandatory : false
- type : float
- name : nopercent
- default : false
- mandatory : false
- type : boolean
- name : gapopen
- default : 10.0
- mandatory : false
- type : float
- name : gapextend
- default : 5.0
- mandatory : false
- type : float
- name : endgaps
- default : false
- mandatory : false
- type : boolean
- name : gapdist
- default : 8
- mandatory : false
- type : long
- name : norgap
- default : false
- mandatory : false
- type : boolean
- name : nohgap
- default : false
- mandatory : false
- type : boolean
- name : maxdiv
- default : 30
- mandatory : false
- type : long
- analysis :
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