SEMPHY 2.0 b3 – Structural EM Phylogenetic Reconstruction

SEMPHY 2.0 b3

:: DESCRIPTION

SEMPHY is a tool for data-intensive phylogenetic reconstruction. SEMPHY infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree.

::DEVELOPER

Nir Friedman’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/ MacOsX

:: DOWNLOAD

SEMPHY

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jan 15;23(2):e136-41.
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates.
Ninio M, Privman E, Pupko T, Friedman N.

Mac5 1.7.3 – Phylogenetic Reconstruction using Gapped Data

Mac5 1.7.3

:: DESCRIPTION

MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite vilification of these models in the literature in the past (e.g., Durbin et al., 1998, p. 217), we have found that, in many circumstances, they are useful for improving the precision of topology estimation.

::DEVELOPER

Grainne McGuire and Paul-Michael Agapow

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

MAC5

:: MORE INFORMATION

Citation:

Gráinne McGuire, Michael C. Denham and David J. Balding
MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps
Bioinformatics (2001) 17 (5): 479-480.

TreSpEx 1.1 – Detection of Misleading Signal in Phylogenetic Reconstructions

TreSpEx 1.1

:: DESCRIPTION

TreSpEx (Tree Space Explorer) combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals.

::DEVELOPER

The Struck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/Windows
Perl

:: DOWNLOAD

TreSpEx

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2014 Mar 31;10:51-67. doi: 10.4137/EBO.S14239. eCollection 2014.
TreSpEx-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information.
Struck TH

SPREAD3 0.9.7 – Spatial Phylogenetic Reconstruction of Evolutionary Dynamics

SPREAD3 0.9.7

:: DESCRIPTION

SPREAD is a user-friendly application to analyze and visualize phylogeographic reconstructions resulting from Bayesian inference of spatio-temporal diffusion.

::DEVELOPER

SPREAD team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/MacOsX/Windows
Java

:: DOWNLOAD

SPREAD

:: MORE INFORMATION

Citation

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.
Bielejec F, Baele G, Vrancken B, Suchard MA, Rambaut A, Lemey P.
Mol Biol Evol. 2016 Aug;33(8):2167-9. doi: 10.1093/molbev/msw082.

Bioinformatics. 2011 Oct 15;27(20):2910-2. doi: 10.1093/bioinformatics/btr481.
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.
Bielejec F, Rambaut A, Suchard MA, Lemey P.