CopyCat 2.04 – Co-phylogenetic Analysis Tool

CopyCat 2.04

:: DESCRIPTION

CopyCat provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies.

::DEVELOPER

Jan P. Meier-KolthoffAlexander F. AuchDaniel H. Huson, and Markus Göker.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

CopyCat

:: MORE INFORMATION

Citation:

Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson, Markus G?ker.
COPYCAT: Co-phylogenetic Analysis tool.
Bioinformatics, 23(7):898-900, 2007.

PAINT 2.24 – Phylogenetic Annotation and INference Tool

PAINT 2.24

:: DESCRIPTION

PAINT is a java application for viewing tree files. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 PAINT

:: MORE INFORMATION

Citation

Brief Bioinform. 2011 Sep;12(5):449-62. Epub 2011 Aug 27.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Gaudet P, Livstone MS, Lewis SE, Thomas PD.

Agalma 1.0.0 – A Transcriptome Assembly and Phylogenetic Analysis Environment

Agalma 1.0.0

:: DESCRIPTION

Agalma is an automated tool that constructs matrices for phylogenomic analyses.  It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.

::DEVELOPER

The Dunn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Agalma

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 19;14:330. doi: 10.1186/1471-2105-14-330.
Agalma: an automated phylogenomics workflow.
Dunn CW1, Howison M, Zapata F.

TreeMap 3.0b – Compare Host & Parasite Trees

TreeMap 3.0b

:: DESCRIPTION

TreeMap is an experimental program for comparing host and parasite trees. TREEMAP performs cophylogeny mapping from a dependent evolutionary tree (e.g., a group of parasites) into an independent one (e.g., the hosts of those parasites), in order to recover the best possible coevolutionary explanation for the relationship between the two . The archetypal example is of the coevolution of pocket gophers and their chewing lice.

::DEVELOPER

Dr. Michael Charleston

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

TreeMap

:: MORE INFORMATION

Citation

M. A. Charleston and D. L. Robertson.
Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny.
Syst Biol, 51(3):528-535, Jun 2002.

MetaTreeMap 3.2 – An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees

MetaTreeMap 3.2

:: DESCRIPTION

MetaTreeMap (MTM) is a module developed to visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.

::DEVELOPER

Laboratory for Integrated Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Javascript

:: DOWNLOAD

 MetaTreeMap

:: MORE INFORMATION

Citation

PLoS One. 2016 Jun 23;11(6):e0158261. doi: 10.1371/journal.pone.0158261. eCollection 2016.
MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees.
Hebrard M, Taylor TD.

RADIS 1.0.0 – Analysis of RAD-seq data for InterSpecific Phylogeny

RADIS 1.0.0

:: DESCRIPTION

RADIS is a perl pipeline which makes the processing of RAD-seq data easier and allows rapid and automated exploration of parameters/data for phylogenetic inference.

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RADIS

:: MORE INFORMATION

Citation

RADIS: Analysis of RAD-seq data for InterSpecific phylogeny.
Cruaud A, Gautier M, Rossi JP, Rasplus JY, Gouzy J.
Bioinformatics. 2016 Jun 16. pii: btw352.

bdvis 0.2.7 – Biodiversity Data Visualizations

bdvis 0.2.7

:: DESCRIPTION

bdvis provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.

::DEVELOPER

Vijay Barve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R

:: DOWNLOAD

 bdvis

:: MORE INFORMATION

Citation

bdvis: visualizing biodiversity data in R.
Barve V, Otegui J.
Bioinformatics. 2016 Jun 10. pii: btw333.

QueTAL 1.1 – A suite for the Functional and Phylogenetic Comparison of TAL effectors

QueTAL 1.1

:: DESCRIPTION

QueTAL is a suite of tools to classify and compare TAL (Transcription Activator-Like) effectors functionally and phylogenetically.

::DEVELOPER

QueTAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  QueTAL

:: MORE INFORMATION

Citation

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically.
Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S, Szurek B, Gagnevin L.
Front Plant Sci. 2015 Aug 3;6:545. doi: 10.3389/fpls.2015.00545.

Bosque 2.0.2 – Phylogenetic Analysis Software

Bosque 2.0.2

:: DESCRIPTION

Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server  can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.

::DEVELOPER

Millenium Institute of Oceanography

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bosque

:: MORE INFORMATION

Citation:

Ramírez-Flandes S. & O. Ulloa(2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541; doi: 10.1093/bioinformatics/btn466

Cocos – Reconstructing Phylogenies of Multi-Domain Proteins

Cocos

:: DESCRIPTION

Cocos is a tool to construct phylogenies of multi-domain proteins.

::DEVELOPER

Research Group Microbial Virulence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 Cocos

:: MORE INFORMATION

Citation

Cocos: Constructing multi-domain protein phylogenies.
Homilius M, Wiedenhoeft J, Thieme S, Standfuß C, Kel I, Krause R.
PLoS Curr. 2011 Jun 9;3:RRN1240. doi: 10.1371/currents.RRN1240.