Tuto Galaxy 2013 : GenOuest, from Fasta to Phylip to Tree to Blast to Filter

Created: 2014-03-05 10:42:19 Last updated: 2014-06-10 09:20:14

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Create a tree from a multifastafile using ClustalW, PhylipDNAdist, PhylipNeighbor, PhylipDrawtree and Treevector, for interactive visualization in Phyloviz or static on pdf or svg format. Then, using the same multifasta file, handling sequences file, use blast on a reference genome and filter results to have sequences with more than 90% identity.

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Workflow Components

Inputs (2)

Name	Description
Multifasta file & query
Reference genome in Fasta format

Steps (17)

Name	Tool	Description
Input dataset	None
Input dataset	None
NCBI BLAST+ blastn	ncbi_blastn_wrapper
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0
Cut	Cut1
Filter fasta sequences	get_seqs
FASTA-to-Tabular	fasta2tab
Join two Datasets	join1
Tabular-to-FASTA	tab2fasta
ClustalW	clustalw
Delines	delines_id
PhylipDNADist	PhylipDNADist
FASTA Width	toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0
PhylipNeighbor	PhylipNJ
Reverse-Complement	toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.0
TreeVector	tree_vector
PhylipDrawtree	PhylipDrawtree

Outputs (18)

Name	Type
output1	tabular
out_file1	input
out_file1	tabular
selected	fasta
unselected	fasta
output	tabular
out_file1	input
output	fasta
output	clustal
outlog	txt
output	data
outfile	txt
output	input
outfile	txt
treefile	nhx
output	input
output	svg
plotfile	pdf

Information Workflow Type

Galaxy

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Ylebras

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Information Statistics

1078 viewings

669 downloads

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Citations (1)

1. Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France, JOBIM 2013, 03 July 2013, https://www.e-biogenouest.org/resources/128

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