PopPhyl protocols

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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

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  • person_outline Nicolas Galtier <>

Publication for PopPhyl

PopPhyl in pipeline

2016
PMCID: 5189939
PMID: 28027292
DOI: 10.1371/journal.pbio.2000234

[…] single pair based on a combination of sequencing coverage and genetic distance criteria, with comparisons between closely related species being favored. raw and final datasets are available from the popphyl website (http://kimura.univ-montp2.fr/popphyl/). sample sizes, number of loci, and source of data are listed in ., for the 51 recently obtained pairs, illumina reads were mapped to predicted […]


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PopPhyl in publications

 (8)
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 […]

PMCID: 5013282
PMID: 27600734
DOI: 10.1038/srep30880

[…] (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)., […]

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 […]

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

[…] 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 […]


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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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