kdetrees 0.1.5 – Nonparametric method for identifying Discordant Phylogenetic Trees

kdetrees 0.1.5

:: DESCRIPTION

kdetrees is a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

::DEVELOPER

Grady Weyenberg and Ruriko Yoshida

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/MacOsX
  • R package

:: DOWNLOAD

 kdetrees

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 24. pii: btu258.
kdetrees: non-parametric estimation of phylogenetic tree distributions.
Weyenberg G, Huggins PM, Schardl CL, Howe DK, Yoshida R.

RidgeRace – Ridge Regression for Continuous Ancestral Character Estimation on Phylogenetic Trees

RidgeRace

:: DESCRIPTION

RidgeRace is a tool to reconstruct ancestral character states and phenotypic rates.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RidgeRace

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):i527-i533. doi: 10.1093/bioinformatics/btu477.
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.
Kratsch C, McHardy AC.

TreeBeST 1.9.2 – Softwares for Phylogenetic Trees

TreeBeST 1.9.2

:: DESCRIPTION

TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.

::DEVELOPER

Heng Li

:: SCREENSHOTS

TreeBeST

:: REQUIREMENTS

  • Windows/Linjux/MacOsX
  • FLTK

:: DOWNLOAD

 TreeBeST

:: MORE INFORMATION

Citation:

Genome Res. 2009 Feb;19(2):327-35. doi: 10.1101/gr.073585.107.
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.

FastCodeML 1.1.0 – Fast Detection of Positive Selection on Phylogenetic Trees

FastCodeML 1.1.0

:: DESCRIPTION

FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol).

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastCodeML

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 23.
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Valle M1, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N.

BayesPhylogenies 1.1 – Inferring Phylogenetic Trees using MCMC or MCMCMC

BayesPhylogenies 1.1

:: DESCRIPTION

BayesPhylogenies is a general package for inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. The program allows a range of models of gene sequence evolution, models for morphological traits, models for rooted trees, gamma and beta distributed rate-heterogeneity, and implements a ‘mixture model’ (Pagel and Meade, 2004) that allows the user to fit more than one model of sequence evolution, without partitioning the data.

::DEVELOPER

Reading Evolutionary Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

  BayesPhylogenies

:: MORE INFORMATION

Citation

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.
Pagel M, Meade A.
Syst Biol. 2004 Aug;53(4):571-81.