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Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data.

Stefanie Hartmann | Conrad Helm | Birgit Nickel | Matthias Meyer | Torsten H Struck | Ralph Tiedemann | Joachim Selbig | Christoph Bleidorn
PloS one | 2012

In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms.

Pubmed ID: 22276131

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Dryad Digital Repository (tool)

RRID:SCR_005910

International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.

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German Research Foundation (tool)

RRID:SCR_012946

German research awards.Central self governing research funding organisation in Germany. Serves sciences and humanities and promotes research at universities and non-university research institutions. The focus is on funding projects developed by academic community.

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RAxML (tool)

RRID:SCR_006086

Software program for phylogenetic analyses of large datasets under maximum likelihood.

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Institute of Bioinformatics and Systems Biology; Neuherberg; Germany (tool)

RRID:SCR_011307

Hosts the Munich Information Center for Protein Sequences (MIPS) and its main focus is the genome-oriented bioinformatics, in particular the systematic analysis of genome information including the development and application of bioinformatics methods in genome annotation, expression analysis and proteomics. MIPS supports and maintains a set of generic databases as well as the systematic comparative analysis of microbial, fungal, and plant genomes.

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German Research Foundation (tool)

RRID:SCR_012420

German research awards.Central self governing research funding organisation in Germany. Serves sciences and humanities and promotes research at universities and non-university research institutions. The focus is on funding projects developed by academic community.

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