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Query : ISEM [tag]

Databases (1)

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


Datasets (3)

Wolbachia complete genome

Wolbachia endosymbiont of Culex quinquefasciatus Pel, complete genome gi|190570478|ref|NC_010981.1|

Author(s)

ISEM


Journal


Tags

ISEM




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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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Ribosomal DNA in vertebrates, angiosperms and other eukaryotes

GC-biased gene conversion impacts ribosomal DNA evolution in vertebrates, angiosperms and other eukaryotes.

Author(s)

Juan S. Escobar, Sylvain Glémin, Nicolas Galtier.


Journal

Molecular biology and evolution


Tags

ISEM




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Softwares (7)

Phylo_win

  

Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes and Cantor, Kimura, Tajima and Nei, HKY, Galtier and Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

Author(s)

Galtier, N., Gouy, M.


Version

2.0


Platform

Linux - Windows - Mac


Source

No


Downloads

0


Tags

ISEM




download

HGT_simul

  

HGT_simul implements the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press) The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes. The user can also control the geometry of the data set: number of taxa, number of genes, sequence lengths, and sampling effort. The input is a (rooted) species tree + an option file setting the parameters of the simulation. The output is a set of genes; for each gene, the simulated alignement and the underlying true gene tree are written in separate files.

Author(s)

Galtier N.


Version

1.2


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Tags

ISEM




download

Identix

  

Permutation test of relatedness

Author(s)

Belkhir K, Castric V, Bonhomme F.


Version

1.1


Platform

Windows


Source

No


Downloads

0


Tags

ISEM




download

Migraine

  

Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. The version available through this page implements only a limited set of models, as described in Rousset and Leblois (2007): essentially a simple model of isolation by distance in a linear habitat, including the island model as a sub-case. The data handled are allelic counts.

Author(s)

François Rousset and Raphaël Leblois


Version

2.0


Platform

Linux


Source

Yes


Downloads

0


Tags

ISEM




download

Partition

  

Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.

Author(s)

Khalid Belkhir and Kevin J. Dawson


Version

2.0


Platform

Windows


Source

No


Downloads

0


Tags

ISEM




download

PartitionML

  

PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.

Author(s)

Khalid Belkhir and François Bonhomme


Version

1


Platform

Windows


Source

No


Downloads

0


Tags

ISEM




download

PopPhyl

Tool

  

The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.

Executables tools

  • Reads2SNP C++ executable (Static compilation for 32, 64 bits Linux and binary for MacOS)(download)
  • dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)(download)
  • ORF extractor perl script (download)
Galaxy-related tools

Author(s)

Nicolas Galtier et al.


Version

1


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Tool - Mapping - Assembler


Tags

ISEM




download

Sources (3)

Baobab

Baobab is an editor for large phylogenetic trees written in Java. ree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier. arge means that Baobab includes tools to simplify the task of managing heavy dataset (typically dealing with several hundred species). Java Development Kit version 1.4.2 minimum.

Langage

JAVA


Downloads

0


Tags

ISEM




download

Genepop

Genepop is a population genetics software package originally developed by Michel Raymond and Francois Rousset, at the Laboratiore de Genetique et Environment, Montpellier, France. Genepop runs under Windows, and can also be compiled to run under Unix or Linux. It will compile on Mac OSX machines if you have the developer tools installed.

Langage

C++


Downloads

0


Tags

ISEM




download

HGT_simul

HGT_simul implements the phylogenomic simulation procedure described in: Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press) The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes. The user can also control the geometry of the data set: number of taxa, number of genes, sequence lengths, and sampling effort. The input is a (rooted) species tree + an option file setting the parameters of the simulation. The output is a set of genes; for each gene, the simulated alignement and the underlying true gene tree are written in separate files.

Langage

C++


Downloads

0


Tags

ISEM




download