Tag: Phylogeny Reconstruction

ForensicEA 1.0 / ForensicEALite 1.0 – Explore the Logic of Phylogeny Reconstruction

ForensicEA 1.0 / ForensicEALite 1.0

:: DESCRIPTION

ForensicEA / ForensicEALite lets the user explore the logic of phylogeny reconstruction. The program creates populations of virus particles. The populations evolve by genetic drift. The user can sample and complare nucleotide sequences from the populations. Various simulations let the user collect and analyze data on: genetic drift within a single population; divergence of populations by drift; and variation among populations on a known phylogeny.

::DEVELOPER

Jon C. Herron

:: SCREENSHOTS

ForensicEA

:: REQUIREMENTS

  • MacOsX / Windows

:: DOWNLOAD

 ForensicEA / ForensicEALite

:: MORE INFORMATION

BIONJ – Distance based Phylogeny Reconstruction Algorithm

BIONJ

:: DESCRIPTION

BIONJ is well suited for distances estimated from DNA or protein sequences. BIONJ has better topological accuracy than NJ in all evolutionary conditions; its superiority becomes important when the substitution rates are high and varying among lineages. However, BIONJ and NJ trees are often close or identical, notably when the number of taxa is low. BIONJ retains the speed of NJ and can be applied to very large data sets (> 1000 taxa). BIONJ can be run on several matrices to build bootstrap trees. As usual, distances should be corrected, e.g. using DNADIST or PROTDIST from PHYLIP.

::DEVELOPER

Olivier Gascuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 BIONJ

:: MORE INFORMATION

Citation

Gascuel O.
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
Molecular Biology and Evolution. 1997 14:685-695.