Tag: Phylogenetic

Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis

Rainbow beta 1.2

:: DESCRIPTION

Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science , Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

D. Chen, O. Eulenstein and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics (2004) 20 (16): 2872-2873.

Phyto-PhyloPars – Phylogenetic approach to the Estimation of Phytoplankton Traits

Phyto-PhyloPars

:: DESCRIPTION

Phyto-PhyloPars web server takes an evolutionary perspective to the variability across phytoplankton taxa in order to estimate the size, maximum growth rate, phosphate affinity and susceptibility to predation of any phytoplankton taxon, based on over one thousand observations on freshwater species.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bruggeman, J. (2011)
A phylogenetic approach to the estimation of phytoplankton traits.
Journal of Phycology 47(1): 52-65.

PhyloCore – Phylogenetic approach to Identifying Core Taxa in Microbial Communities

PhyloCore

:: DESCRIPTION

PhyloCore is an application that uses a phylogeny-based algorithm to identify the core microbiota taxa at the proper taxonomic levels.

::DEVELOPER

Wu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

PhyloCore

:: MORE INFORMATION

Citation

Ren T, Wu M.
PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities.
Gene. 2016 Nov 30;593(2):330-3. doi: 10.1016/j.gene.2016.08.032. Epub 2016 Aug 24. PMID: 27567683; PMCID: PMC5037057.

DendroPy v4.5.1 – Phylogenetic Computing Library

DendroPy v4.5.1

:: DESCRIPTION

DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.

::DEVELOPER

Sukumaran Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

  DendroPy

:: MORE INFORMATION

Citation:

Sukumaran, J. and Mark T. Holder. 2010.
DendroPy: A Python library for phylogenetic computing.
Bioinformatics 26: 1569-1571.

G-PhoCS – Generalized Phylogenetic Coalescent Sampler

G-PhoCS

:: DESCRIPTION

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

::DEVELOPER

Siepel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

G-PhoCS

 :: MORE INFORMATION

Citation

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.
Bayesian inference of ancient human demography from individual genome sequences.
Nat Genet. 2011 Sep 18;43(10):1031-4. doi: 10.1038/ng.937. PMID: 21926973; PMCID: PMC3245873.

TargetOrtho 2.0 – A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets

TargetOrtho 2.0

:: DESCRIPTION

TargetOrtho provides a cost- and time-efficient in silico approach for the identification of novel TF target genes, and, together with its CRM search function, is poised to unravel the regulatory logic of diverse biological processes.

::DEVELOPER

Hobert Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 TargetOrtho

:: MORE INFORMATION

Citation

Genetics. 2014 May;197(1):61-76. doi: 10.1534/genetics.113.160721. Epub 2014 Feb 20.
TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.
Glenwinkel L1, Wu D, Minevich G, Hobert O.

Clann 4.2.5 – Construct Phylogenetic Supertrees

Clann 4.2.5

:: DESCRIPTION

Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Clann

:: MORE INFORMATION

Citation:

Creevey C. J. and McInerney, J. O. 2005
Clann: Investigating phylogenetic information through supertree analyses.
Bioinformatics 21 (3): 390-2.

FOOTER 2.0 – Find Ammalian Transcription Factor Binding Sites using Phylogenetic Footprinting

FOOTER 2.0

:: DESCRIPTION

FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

EBD 1.0.8 – Taxon- and Phylogenetic-based Beta Diversity Measures

EBD 1.0.8

:: DESCRIPTION

EBD (Express Beta Diversity) is a software package for calculating measures of taxon- or phylogenetic-based beta diversity.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

  EBD

:: MORE INFORMATION

Citation

Parks, D.H. and Beiko, R.G.
Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.
ISME J. 2013 Jan;7(1):173-83

treecat – Phylogenetic Comparative Assembly

treecat

:: DESCRIPTION

treecat (phylogenetic tree based contig arrangement tool) takes several genomes and their relationships in a phylogenetic tree into account to estimate a possible ordering of the contigs.

::DEVELOPER

treecat team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

treecat

:: MORE INFORMATION

Citation

Husemann, P. & Stoye, J.
Phylogenetic comparative assembly
Algorithms for Molecular Biology, 2010, Vol. 5(1), pp. 3

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