jMODELTEST 2.1.10 – Phylogenetic Model Averaging

jMODELTEST 2.1.10

:: DESCRIPTION

jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies. Please note that the DT weights are very gross.

jModelTest2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimization, model-averaged phylogenetic trees (both topology and branch length), heuristic filtering and automatic logging of user activity.

::DEVELOPER

Posada Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOS
Java

:: DOWNLOAD

jMODELTEST

:: MORE INFORMATION

Citation

Posada D. 2008.
jModelTest: Phylogenetic Model Averaging.
Molecular Biology and Evolution 25: 1253-1256.

Darriba D, Taboada GL, Doallo R, Posada D. 2012.
jModelTest 2: more models, new heuristics and parallel computing.
Nature Methods 9(8), 772.

misfits 1.0 – Evaluate Goodness of Fit between Phylogenetic Model and Alignment

misfits 1.0

:: DESCRIPTION

misfits is a computer program to evaluate the goodness of fit between a phylogenetic model and an alignment.It offers a look back at the alignment to pinpoint to site patterns that do not fit to the model and the resulting tree (thereafter referred to as the tree-model). MISFITS then introduces a number of extra-substitutions on the tree, in a parsimonious manner to fit these site patterns in to the tree-model. These extra-substitutions plus the evolutionary model will then fully explain the alignment. Thus, the number of extra-substitutions may be interpreted as a measure to evaluate the goodness of fit of the model to the alignment: the less the number, the better the fit.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX

:: DOWNLOAD

misfits

:: MORE INFORMATION

Citation:

Minh Anh Thi Nguyen, Steffen Klaere, and Arndt von Haeseler (2010)
MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment.
Mol. Biol. Evol., 28:143-152.