PopPhyl

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]