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Items tagged with "phylogenetic tree" (8)

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Workflows (6)

Taverna 1 Original Uploader M.B.Mon...	Workflow for Protein Sequence Analysis (v1) Created: 09/01/08 @ 12:03:03 \| Last updated: 09/01/08 @ 12:31:27 Credits: M.B.Monteiro Attributions: BLAST using DDBJ service Simplify a BLAST text file conditional branch License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 4.0 / 5 (2 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 1615 times \| Downloaded: 430 times Tags (10): analysis \| BLAST \| homology \| multiple sequence alignment \| phylogenetic tree \| protein \| sequence \| tree \| wpsa	View Download (v1)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW2_phylogentic_tree (v2) Created: 07/04/09 @ 20:09:32 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2). Rating: 4.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 1 \| Comments: 1 \| Citations: 0 Viewed: 280 times \| Downloaded: 102 times Tags (7): bioinformatics \| clustal \| clustalw \| ebi \| neighbor-joining \| phylogenetic tree \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	EBI_ClustalW_alignment_tree (v2) Created: 31/05/08 @ 13:53:04 \| Last updated: 03/12/10 @ 13:34:43 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree License: Creative Commons Attribution 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 176 times \| Downloaded: 83 times Tags (10): alignment \| bioinformatics \| clustal \| clustalw \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| sequence alignment \| tree	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Protein_search_fetch_align_tree (v2) Created: 07/04/09 @ 20:13:19 Credits: Hamish McWilliam Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST License: Creative Commons Attribution 3.0 Unported License An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 419 times \| Downloaded: 140 times Tags (15): alignment \| bioinformatics \| BLAST \| clustal \| clustalw \| dbfetch \| ebi \| multiple sequence alignment \| neighbor-joining \| phylogenetic tree \| protein \| sequence alignment \| sequence similarity search \| tree \| wu-blast	View Download (v2)
BioExtract Server Original Uploader Carol Lushbough	Phylogeny Bootstrapped Algorithm (v2) Created: 13/01/10 @ 18:47:06 \| Last updated: 17/11/10 @ 13:57:19 Credits: Carol Lushbough License: Creative Commons Attribution-Share Alike 3.0 Unported License Bootstrapped sequences algorithm reads in a data set, and produces multiple data sets from it by bootstrap resampling. http://pro.genomics.purdue.edu/cgi-bin/emboss/help/fseqboot Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 204 times \| Downloaded: 130 times Tags (5): bioextract \| bootstrapp \| nucleotide \| phylogenetic tree \| phylogeny	View Download (v2)
Taverna 1 Original Uploader Achille Zappa	MY_Multi_Alignment_Phylo (v1) Created: 03/11/09 @ 14:46:38 Credits: Achille Zappa License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 137 times \| Downloaded: 37 times Tags (7): clustalw \| ml \| multiple alignment \| muscle \| nj \| phylogenetic tree \| upgma	View Download (v1)

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Creator:

Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:04:23 | Last updated: 07/08/09 @ 16:23:53

A tutorial to demonstrate how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

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Uploader:

Carol Lushbough

BioExtract Server Workflow Tutorial

Created: 07/08/09 @ 16:20:06 | Last updated: 07/08/09 @ 16:25:46

Credits: Carol Lushbough

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This tutorial demonstrates how to create a workflow within the BioExtract Server at bioextract.org. Specifically, it shows how to perform a phylogenetic analysis on a set of proteins where the starting point is a query for specific nucleotide gene sequences.

File type: Word 2007 document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 29 times | Downloaded: 25 times

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