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PopPhyl specifications

Information


Unique identifier OMICS_16103
Name PopPhyl
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Perl, Shell (Bash)
Computer skills Advanced
Stability Stable
Source code URL https://kimura.univ-montp2.fr/PopPhyl/resources/tools/popphyl_tools.tar.gz
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Nicolas Galtier

Publication for PopPhyl

PopPhyl citations

 (4)
library_books

Range expansion underlies historical introgressive hybridization in the Iberian hare

2017
Sci Rep
PMCID: 5264399
PMID: 28120863
DOI: 10.1038/srep40788

[…] 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 was constructed using Trinity v.2.1.0 with defa […]

library_books

Discovery of parvovirus related sequences in an unexpected broad range of animals

2016
Sci Rep
PMCID: 5013282
PMID: 27600734
DOI: 10.1038/srep30880

[…] n (Uniprot) databases. We also used these as queries to screen, eleven new transcriptomes generated from invertebrate datasets provided by N. Galtier (European Research Council advanced grant 232971 (PopPhyl)). All hits were next selected and used as queries to perform BLASTX or BLASTP reciprocal searches of the NCBI non-redundant sequence database (as described in the materials and methods).Three […]

library_books

Reference Free Population Genomics from Next Generation Transcriptome Data and the Vertebrate–Invertebrate Gap

2013
PLoS Genet
PMCID: 3623758
PMID: 23593039
DOI: 10.1371/journal.pgen.1003457

[…] amplification during library preparation –. Details of the method and simulations are provided in . The reads2snps SNP-caller and paralogue filter can be downloaded from http://kimura.univ-montp2.fr/PopPhyl/resources/tools/reads2snp.tar.gz.Outgroup sequences were added to these alignments, when available. To achieve this aim, Illumina reads from the outgroup species were assembled using Abyss and […]

library_books

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

2012
BMC Biol
PMCID: 3473239
PMID: 22839781
DOI: 10.1186/1741-7007-10-65

[…] atics Biodiversity platform. We are grateful to the three anonymous reviewers for their helpful comments. This project was supported by a European Research Council (ERC) grant to Nicolas Galtier (ERC PopPhyl 232971). YC has been partially supported by a FCT postdoctoral fellowship SFRH/BPD/73515/2010. This work is contribution ISEM 2012-083 of the Institut des Sciences de l'Evolution de Montpellie […]

Citations

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PopPhyl funding source(s)
This work was supported by a European Research Council (ERC) grant (ERC PopPhyl 232971), partially by a FCT postdoctoral grant SFRH⁄BPD⁄73515⁄2010, and by a post-doc grant from FCT with reference SFRH⁄BPD⁄43264⁄2008.

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