PhyloGenie protocols

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PhyloGenie specifications

Information


Unique identifier OMICS_13098
Name PhyloGenie
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
BLAST, Formatdb, Java
Maintained Yes

Taxon


  • Vertebrates
    • Danio rerio

Versioning


Add your version

Maintainer


  • person_outline Andrei Lupas <>

Publication for PhyloGenie

PhyloGenie in pipeline

2007
PMCID: 2064935
PMID: 17894863
DOI: 10.1186/1471-2148-7-173

[…] shared by dinoflagellates. the 3,341 sequences were translated into the six open reading frames using the transeq program in the emboss package [] and used as input for the analysis with the phylogenie package of computer programs []. phylogenie serves as an automated pipeline in which the following analyses can be implemented: blast search against a local database, extraction […]


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PhyloGenie in publications

 (17)
PMCID: 5264399
PMID: 28120863
DOI: 10.1038/srep40788

[…] leading:5 trailing:5 slidingwindow:4:15 minlen:20. previously published transcriptome single-end sequence reads from 10 l. granatensis specimens (data available from ftp://ngsisem.mbb.univ-montp2.fr/phylogenie_et_evolution_moleculaire/pub/popphyl/reads/lepus_granatensis/) were added to the dataset (see geographic distribution of the 11 sampled specimens in )., de novo transcriptome assembly […]

PMCID: 4973528
PMID: 27492357
DOI: 10.1186/s13062-016-0137-2

[…] differential loss in some archaeal phyla and in eukarya. this could explain for instance why eukarya are more related to particular archaeal phyla in the trees of figs. , and . unfortunately, the phylogenie are difficult to interpret because jonathan lombard also uses many fast evolving species in his dataset. for instance, nanoarchaeaum and the korarchaeon in fig. , methanopyrus kandleri […]

PMCID: 5448076
PMID: 28596624
DOI: 10.1007/s12542-016-0313-9

[…] vorliegenden morphometrischen daten, dass bourgueticrinus ellipicus und b.? suedicus konspezifisch sind. taphonomie und paläoökologie der crinoiden-vergesellschaftung werden diskutiert, wie auch die phylogenie der kreidezeitlichen bourgueticriniden revidiert wird., the online version of this article (doi:10.1007/s12542-016-0313-9) contains supplementary material, which is available to authorized […]

PMCID: 4526936
PMID: 26070951
DOI: 10.2196/jmir.4415

[…] supporting scientists in the design of new dna molecules. also, several tabletop systems have also been developed to explore interactive visualization of large biological datasets—deeptree [] and phylogenie [] allow users to explore and learn phylogenetic trees. most closely related to our work is g-nome surfer [], a tabletop user interface for collaborative exploration and learning […]

PMCID: 4276288
PMID: 25179679
DOI: 10.1002/eji.201344421

[…] had more than one mutation, all mutations had to pass above threshold. custom r and perl scripts were used at all steps. genealogical relations and phylogenetic trees were generated using the phylogenie.fr online tool ., statistical analysis was performed with ibm spss 20 and graphpad prism 5. mann–whitney test (nonnormally distributed samples), paired student's t-tests (normally […]


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PhyloGenie institution(s)
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tuebingen, Germany

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