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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
Reference-free transcriptome assembly in non-model animals from next-generation sequencing data.
PopPhyl citations
(4)Range expansion underlies historical introgressive hybridization in the Iberian hare
[…] 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 […]
Discovery of parvovirus related sequences in an unexpected broad range of animals
[…] 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 […]
Reference Free Population Genomics from Next Generation Transcriptome Data and the Vertebrate–Invertebrate Gap
[…] 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 […]
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
[…] 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 […]
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