Tag: Phylogenomic

HGT_simul 1.2 – Phylogenomic Simulation

HGT_simul 1.2

:: DESCRIPTION

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.

::DEVELOPER

Nicolas Galtier – galtier@univ-montp2.fr

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows / Linux/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 HGT_simul

:: MORE INFORMATION

Syst Biol. 2007 Aug;56(4):633-42.
A model of horizontal gene transfer and the bacterial phylogeny problem.
Galtier N.

PALEOMIX 1.3.2 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.3.2

:: DESCRIPTION

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PALEOMIX

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M1, Ermini L1, Der Sarkissian C1, Jónsson H1, Ginolhac A1, Schaefer R2, Martin MD1, Fernández R1, Kircher M3, McCue M4, Willerslev E1, Orlando L1.