ANGST – ANalyzer of Gene and Species Trees

ANGST

:: DESCRIPTION

AnGST performs a phylogenetic reconciliation between a given species and gene tree, positing the best scoring set of HGT, DUP, and LOS events to explain all topological incongruities between the two trees. In order to protect against phylogenetic noise, we have designed AnGST to be capable of incorporating information from dozens of bootstrap trees simultaneously. In cases of variations among bootstrap subtrees, the subtree that best accords with the reference tree is adopted.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
Python

:: DOWNLOAD

ANGST

:: MORE INFORMATION

Citation

LA David & EJ Alm.
“Rapid evolutionary innovation during an Archaean Genetic Expansion.”
Nature, 2010. doi:10.1038/nature09649.

TreeFix 1.1.10 / TreeFix-DTL 1.0.2 – Statistically Informed Gene Tree Error Correction using Species Trees

TreeFix 1.1.10 / TreeFix-DTL 1.0.2

:: DESCRIPTION

TreeFix is a phylogenetic method for improving gene tree reconstructions using a test statistic for likelihood equivalence and a species tree aware (reconciliation) cost function.

TreeFix-DTL is a phylogenetic program for reconstructing highly accurate prokaryotic gene trees.

::DEVELOPER

Yi-Chieh Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
C Compiler

:: DOWNLOAD

TreeFix / TreeFix-DTL

:: MORE INFORMATION

Citation

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, and Manolis Kellis.
Systematic Biology. 2013. doi: 10.1093/sysbio/sys076

Improved Gene Tree Error-Correction in the Presence of Horizontal Gene Transfer.
Bansal MS, Wu YC, Alm EJ, Kellis M.
Bioinformatics. 2014 Dec 5. pii: btu806.

COALGF Calculator 1.0 – Computing Probabilities of Gene Tree Histories Given Species Trees Under the Coalescent Process with Gene Flow

COALGF Calculator 1.0

:: DESCRIPTION

COALGF Calculator is a C program that will compute the probability distribution of gene tree histories and gene tree topolgies for a fixed three-taxon species tree under the coalescent model with gene flow between both pairs of sister population.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

COALGF Calculator

:: MORE INFORMATION

Citation

Distribution of coalescent histories under the coalescent model with gene flow.
Tian Y, Kubatko LS.
Mol Phylogenet Evol. 2016 Dec;105:177-192. doi: 10.1016/j.ympev.2016.08.024.

urRF – unrooted Gene Trees vs rooted Species Trees

urRF

:: DESCRIPTION

urRF is a new measure based on the standard RF (Robinson-Foulds) distance to compare an unrooted tree with a rooted tree, and describe a linear time algorithm to compute urRF.

:DEVELOPER

Paweł Górecki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

urRF

:: MORE INFORMATION

Citation:

Paweł Górecki, Oliver Eulenstein
A Robinson-Foulds measure to compare unrooted trees with rooted trees
Bioinformatics Research and Applications Lecture Notes in Computer Science Volume 7292, 2012, pp 115-126