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.

Clann 4.2.4 – Construct Phylogenetic Supertrees

Clann 4.2.4

:: 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.

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

PhyloSift 1.0.1 – Phylogenetic and Taxonomic Analysis for Genomes and Metagenomes

PhyloSift 1.0.1

:: DESCRIPTION

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

 PhyloSift

:: MORE INFORMATION

Citation

PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.
PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243.

SPECTRE 1.1.5 – Suite of Phylogenetic tools for Reticulate Evolution

SPECTRE 1.1.5

:: DESCRIPTION

SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SPECTRE 

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Mar 15;34(6):1056-1057. doi: 10.1093/bioinformatics/btx740.
SPECTRE: a suite of phylogenetic tools for reticulate evolution.
Bastkowski S, Mapleson D, Spillner A, Wu T, Balvociute M, Moulton V.

JPhyloIO 1.0.0 – Reading and Writing of different Phylogenetic File Formats

JPhyloIO 1.0.0

:: DESCRIPTION

JPhyloIO is an open source Java library for reading and writing phylogenetic file formats. The main aim is to provide access to various formats using a single interface, while being independent of the concrete application data model, to achieve maximal flexibility.

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

JPhyloIO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2019 Jul 22;20(1):402. doi: 10.1186/s12859-019-2982-3.
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface.
Stöver BC, Wiechers S, Müller KF.

PhyDE2 0.2.0 – Phylogenetic Data Editor

PhyDE2 0.2.0

:: DESCRIPTION

PhyDE (Phylogenetic Data Editor) is a system-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

PhyDE

:: MORE INFORMATION

PhyloGena 1.04 – Automated Interactive Phylogenetic Annotation Tool

PhyloGena 1.04

:: DESCRIPTION

PhyloGena is a software tool to facilitate phylogenetic annotation of unknown sequences. It has a user-friendly graphical interface and you will intuitively learn how to use it. You can import 1, 10, 100, 1000? (see below) DNA or protein sequences and the program will search for similar sequences, construct a multiple alignment and subsequently a phylogenetic tree for all of them and show them to you. You can easily manipulate the data sets, add or remove sequences, change parameters etc. This is of great help in identifying the function and phylogenetic affiliation of ORFs and makes annotation of genes or ESTs easier and less error-prone.

::DEVELOPER

PhyloGena Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

PhyloGena

:: MORE INFORMATION

Citation:

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.
PhyloGena–a user-friendly system for automated phylogenetic annotation of unknown sequences.
Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.

PhyMAIT – Phylogenetic Multiple Alignment Improvement Tool

PhyMAIT

:: DESCRIPTION

PhyMAIT is a Phylogenetic Multiple Alignment Improvement Tool

::DEVELOPER

Hongtao Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PhyMAIT

:: MORE INFORMATION

Citation

H.Sun and J. Buhler,
PhyMAIT – a Phylogenetic Multiple Alignment Improvement Tool
(in preparation)