MY_Multi_Alignment_Phylo

Created: 2009-11-03 14:46:38

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This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis.

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Workflow Components

Inputs (1)

Name	Description
Sequences_or_IDs

Processors (18)

Name	Type	Description
Extract_Seq_Description	beanshell
Get_Proteins_FASTA	workflow	Given a sequence or sequence entry identifer return the sequence in fasta format. If a sequence identifier is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.
ClustalW2	workflow	Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.
Clustal_Tcoffee	workflow	Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSToffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) ise used.
Muscle	workflow	Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used.
Nested_Workflow4	workflow
Nested_Workflow5	workflow
ClustalW	soaplabwsdl	Multiple alignment program - interface to ClustalW program
Nested_Workflow6	workflow
Nested_Workflow10	workflow
Nested_Workflow8	workflow
Nested_Workflow3	workflow
Nested_Workflow1	workflow	This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.
Nested_Workflow2	workflow	This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.
Nested_Workflow9	workflow
Nested_Workflow11	workflow
Nested_Workflow	workflow	This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.
Nested_Workflow7	workflow

Beanshells (7)

Name	Description	Inputs	Outputs
Beanshell		in	out
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence
Is_done	Map job status into true/false is done flag	job_status	is_done
Is_done	Map job status into true/false is done flag	job_status	is_done
Is_done	Map job status to true/false	job_status	is_done
Is_done	Convert status code into true/false.	job_status	is_done
Extract_Seq_Description		Sequences	result

Outputs (32)

Name	Description
Protein Description
ClustalW_UPGMA
Distance Outfile
Muscle_Alignment
ClustalW2 result
ClustalW2 Alignment
ClustalW2_phylip_tree
emma result
Clustal T-coffee alignment
ClustalW2_nj_tree
ClustalW2 NJ
ClustalW2 dist-out
ClustalW2 UPGMA
ClustalW2 u-dist-out
ClustalW NJ
ClustalW n-dist-out
1
2
3
4
6
7
8
5
Muscle UPGMA
Muscle u-dist
Muscle NJ
Muscle nj-dist
CW_T-coffee UPGMA
CW_T-coffee u-dist
CW_Tcoffee NJ
CW_Tcoffee nj-dist

Links (50)

Source	Sink
ClustalW2:ClustalW_alignment	Nested_Workflow1:Alignments
ClustalW2:ClustalW_alignment	Nested_Workflow3:Alignments
ClustalW2:ClustalW_alignment	Nested_Workflow:Alignments
ClustalW:outseq	Clustal_Tcoffee:Sequences
ClustalW:outseq	Nested_Workflow11:Alignments
ClustalW:outseq	Nested_Workflow2:Alignments
ClustalW:outseq	Nested_Workflow5:Alignments
Sequences_or_IDs	Get_Proteins_FASTA:Sequences_or_IDs
Clustal_Tcoffee:TCoffee_alignment	Nested_Workflow10:Alignments
Clustal_Tcoffee:TCoffee_alignment	Nested_Workflow6:Alignments
Clustal_Tcoffee:TCoffee_alignment	Nested_Workflow9:Alignments
Get_Proteins_FASTA:sequences	ClustalW2:Sequences
Get_Proteins_FASTA:sequences	ClustalW:sequence_direct_data
Get_Proteins_FASTA:sequences	Extract_Seq_Description:Sequences
Get_Proteins_FASTA:sequences	Muscle:Sequences
Muscle:MUSCLE_alignment	Nested_Workflow7:Alignments
ClustalW2:ClustalW_alignment	ClustalW2 Alignment
ClustalW2:ClustalW_nj_tree	ClustalW2_nj_tree
ClustalW2:ClustalW_output	ClustalW2 result
ClustalW2:ClustalW_phylip_tree	ClustalW2_phylip_tree
ClustalW:outseq	emma result
Clustal_Tcoffee:TCoffee_alignment	Clustal T-coffee alignment
Extract_Seq_Description:result	Protein Description
Muscle:MUSCLE_alignment	Muscle_Alignment
Muscle:MUSCLE_alignment	Nested_Workflow4:Alignments
Muscle:MUSCLE_alignment	Nested_Workflow8:Alignments
Nested_Workflow10:Distance	CW_Tcoffee nj-dist
Nested_Workflow10:NJ	CW_Tcoffee NJ
Nested_Workflow11:Distance	Distance Outfile
Nested_Workflow11:UPGMA	ClustalW_UPGMA
Nested_Workflow1:Distance	ClustalW2 u-dist-out
Nested_Workflow1:UPGMA	ClustalW2 UPGMA
Nested_Workflow2:Distance	ClustalW n-dist-out
Nested_Workflow2:NJ	ClustalW NJ
Nested_Workflow3:ML_tree	4
Nested_Workflow3:Max-Like	3
Nested_Workflow4:ML_tree	6
Nested_Workflow4:Max-Like	5
Nested_Workflow5:ML_tree	8
Nested_Workflow5:Max-Like	7
Nested_Workflow6:ML_tree	2
Nested_Workflow6:Max-Like	1
Nested_Workflow7:Distance	Muscle nj-dist
Nested_Workflow7:NJ	Muscle NJ
Nested_Workflow8:Distance	Muscle u-dist
Nested_Workflow8:UPGMA	Muscle UPGMA
Nested_Workflow9:Distance	CW_T-coffee u-dist
Nested_Workflow9:UPGMA	CW_T-coffee UPGMA
Nested_Workflow:Distance	ClustalW2 dist-out
Nested_Workflow:NJ	ClustalW2 NJ

Coordinations (11)

Controller	Target
Nested_Workflow3	Nested_Workflow
Nested_Workflow	Nested_Workflow1
Nested_Workflow1	Muscle
Nested_Workflow4	Nested_Workflow7
Nested_Workflow7	Nested_Workflow8
Nested_Workflow8	ClustalW
Nested_Workflow5	Nested_Workflow2
Nested_Workflow2	Nested_Workflow11
Nested_Workflow11	Clustal_Tcoffee
Nested_Workflow6	Nested_Workflow9
Nested_Workflow9	Nested_Workflow10

Information Workflow Type

Taverna 1

Information Uploader

Achille Zappa

Information License

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Information Version 1 (of 1)

Information Credits (1)

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Achille Zappa

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Information Statistics

2151 viewings

1666 downloads

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Version History

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MY_Multi_Alignment_Phylo

Created by Achille Zappa on Tuesday 03 November 2009 14:46:46 (UTC)

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