Uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow. GeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise gene families, produced using the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

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GeneSeqToFamily classification

GeneSeqToFamily specifications

Software type:
Pipeline
Restrictions to use:
None
Input format:
JSON
Programming languages:
Javascript, Perl, Python
Stability:
Stable
Interface:
Command line interface
Input data:
Coding sequences (CDS) to protein sequences, a species tree, gene feature information in JSON format
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Requirements:
Transeq, Filter by FASTA IDs, BLAST, BLAST parser, hcluster_sg, hcluster_sg parser, T-Coffee, Tranalign, TreeBeST, Gene Alignment and Family Aggregator (GAFA), cut, Ensembl REST API, gff3-to-json

Publications

  • (Thanki et al., 2016) GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow. bioRxiv.
    DOI: 10.1101/096529

Credits

Institution(s)

Earlham Institute (EI), Norwich Research Park, Norwich, UK; EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK

Funding source(s)

This research was supported in part by the NBI Computing infrastructure for Science (CiS) group.

Link to literature

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