clan_check v1.3 – Check Trees for compatibility with Defined Clans

clan_check v1.3

:: DESCRIPTION

Clan_Check analyses single-copy phylogenetic trees to assess if they violate clans defined by the user. This is designed for large-scale phylogenomic analyses where the user may have thousands of phylogenetic trees. This tool can help enrich the data for orthologs, by identifying where paralogy has caused violation of “well known” clans in outgroups.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Clan_Check

:: MORE INFORMATION

Citation

Siu-Ting, Karen, et al.
Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics.
Molecular biology and evolution (2019).

TreeSim 2.4 / TreeSimGM 2.3 – Simulating Trees under the Birth-Death Model / under a General Model

TreeSim 2.4 / TreeSimGM 2.3

:: DESCRIPTION

TreeSim is an R package for simulating phylogenetic trees.

TreeSimGM: Simulating Phylogenetic Trees under a General Model

::DEVELOPER

Computational Evolution group at ETH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX
R package

:: DOWNLOAD

TreeSim , TreeSimGM

:: MORE INFORMATION

Citation

Syst Biol. 2011 Oct;60(5):676-84. doi: 10.1093/sysbio/syr029. Epub 2011 Apr 11.
Simulating trees with a fixed number of extant species.
Stadler T.

BEAGLE 3.1.2 – Evaluating the Likelihood of Sequence Evolution on Trees

BEAGLE 3.1.2

:: DESCRIPTION

BEAGLE-lib (Broad-platform Evolutionary Analysis General Likelihood Evaluator) is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.

::DEVELOPER

BEAGLE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

BEAGLE

:: MORE INFORMATION

Citation

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.
Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Landmark 3.6 – 3D Morphological Models on Trees

Landmark 3.6

:: DESCRIPTION

The main purpose of Landmark is to easily place landmark points and semi-landmark points accurately and with high repeatability on complex surfaces for the purpose of registration, alignment, morphing, and computation of hypothetical ancestors in evolutionary trees.

::DEVELOPER

The Institute for Data Analysis and Visualization

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Landmark

:: MORE INFORMATION

Citation

David F. Wiley, Nina Amenta, Dan A. Alcantara, Deboshmita Ghosh, Yong J Kil, Eric Delson, Will Harcourt-Smith, F. James Rohlf, Katherine St. John, Bernd Hamann,
Evolutionary Morphing,
Visualization, 2005. VIS 05. IEEE Page(s): 431 – 438