PopPhyl

[…] 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 […]

[…] 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 […]

[…] (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)., […]

[…] useful advice and the montpellier bioinformatics & biodiversity platform for support regarding computational aspects. this work was supported by european research council advanced grant 232971 (popphyl) and agence nationale de la recherche grant anr-10-binf-01-01 […]

[…] 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 […]

[…] 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 […]