Data Phylogenomics

Databases and Datasets

Databases

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Arbre de la vie

 

L’arbre de la vie est un projet de l'Université Montpellier II.
Il a pour but de mettre à disposition des étudiants et des enseignants les connaissances actuelles sur la diversité du vivant. Le site propose de naviguer entre les grands groupes taxonomiques grâce à des arbres cliquable. Pour accéder aux informations disponible pour un taxon, cliquez sur son nom dans l’arbre. Pour naviguer entre les arbres cliquez sur les flèches : une flèche à la racine de l’arbre permet de remonter vers l’arbre parent ; une flèche à droite d’un nom de taxon permet d’afficher l’arbre dont ce taxon est l’ancêtre commun. Toutes les informations présentées dans ce site peuvent être librement exploitées.

Tags

Apps


OrthoMaM

 

Molecular data play a key role in phylogenetic inference. Mammalian systematics provides us with a clear example, with several previously open evolutionary questions now able to be answered. However, molecular studies have until present used only a handful of classic markers and have not attempted to utilise the information contained within the increasingly large pool of mammalian genome sequences. The identification and utilisation of potentially new informative markers from this pool can help to further resolve the mammalian phylogenetic tree.

Tags

Mammalian - ISEM


Polymorphix

 

Polymorphix is a database of intraspecific sequence polymorphism, structured under the ACNUC sequence database management system. It allows one to select sets of within-(eukaryotic)species sequences families, and to visualize multiple alignments and phylogenetic trees. Polymorphix is useful for meta-analyses of population genomics, and as a bibliographic tool in population genetics. Families in Polymorphix are groups of sequences sharing at least 80% similarity. Multiple alignments were made with Mabios. Outgroup have been added when available (78% similarity required), and aligned to the within-species profile with Clustalv-1.81. Sequence alignments and Neighbour-Joining phylogenetic trees can be viewed. You can use them, together with sequence annotations and bibliographic links, to decide wether the selected families are relevant for your study




Datasets

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An evolutionary genome scan for longevity-related natural selection in mammals

Nucleotide sequence alignments: 10,762 nuclear-coding genes across 15-25 Mammalian species.

  • ISEM 2009-143: An evolutionary genome scan for longevity-related natural selection in mammals.
  • Mol Biol Evol. 2010 Apr;27(4):840-7. Epub 2009 Dec 2.
  • PMID: 19955481 [PubMed - indexed for MEDLINE]

Author(s)

Jobson RW, Nabholz B, Galtier N.


Journal

Molecular biology and evolution


Tags

ISEM




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Determinism of mitochondrial genetic diversity in mammals

Mammalian polymorphism data

Author(s)

Nabholz B, Mauffrey JF, Bazin E, Galtier N, Glemin S.


Journal

Genetics




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GC-biased segregation of non-coding polymorphisms in Drosophila

Drosophila data sets, GC-biased segregation of non-coding polymorphisms in Drosophila. Genetics 2005

Author(s)

Galtier N., Bazin E. and Bierne N


Journal

Genetics




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Impact of mating systems on patterns of sequence polymorphism in flowering plants

Impact of mating systems on patterns of sequence polymorphism in flowering plants Sylvain Glemin,Eric Bazin and Deborah Charlesworth Proc. Roy. Soc. 2006.

Author(s)

Sylvain Glemin,Eric Bazin and Deborah Charlesworth


Journal

Proc. Roy. Soc.




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Mutation hot spots in mammalian mitochondrial DNA

Mammalian mitochondrial data. Mutation hot spots in mammalian mitochondrial DNA. [2008] Genome Research 16:215-222. - Aligned Hominoidea mitochondrial coding region : alg_primates-hommes.fasta - Aligned cytochrome b in 113 species from 66 mammalian genera : mammalian_cytb.tar.gz

Author(s)

Galtier N., Enard D., Radondy Y., Bazin E. and Belkhir K.


Journal

Genome Research




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