Tag: Phylogenetic Tree

RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program

RadCon 1.1.6

:: DESCRIPTION

RadCon is a phylogenetic tree consensus and comparison program for Macs (OS 7.5 – 9).Implemented methods include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.

::DEVELOPER

RadCon team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac(OS 7.5 – 9)

:: DOWNLOAD

 RadCon

:: MORE INFORMATION

Citation

Joseph L. Thorley and Roderic D. M. Page
RadCon: phylogenetic tree comparison and consensus
Bioinformatics (2000) 16 (5): 486-487.

PhyloSNP – Take SNP data files (.csv and .vcf) and Generate Phylogenetic Trees

PhyloSNP

:: DESCRIPTION

PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data. Additionally, PhyloSNP can either generate a shortened concatenated genome from the SNPs or generate a concatenated genome from contigs generated from the SNPs and a specified number of base pairs around each SNP.

::DEVELOPER

High-performance Integrated Virtual Environment (HIVE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

  PhyloSNP

:: MORE INFORMATION

Citation

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.
Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.
Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R

NewickReader 1.0 – Produce Distance Matrix from Branch Lengths in Phylogenetic Tree

NewickReader 1.0

:: DESCRIPTION

NewickReader is a program for producing a distance matrix from the branch lengths in a phylogenetic tree in newick format. The program reads the branch lengths of a phylogenetic tree in standard newick format, adds them up to produce the total distances between taxa within the phylogeny, and outputs a symmetrical matrix.

::DEVELOPER

The ASJP project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  NewickReader

:: MORE INFORMATION

PhyloTreePruner – A Nifty Java program for Pruning Phylogenetic Trees

PhyloTreePruner

:: DESCRIPTION

PhyloTreePruner is a utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.

::DEVELOPER

Halanych Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 PhyloTreePruner

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Oct 29;9:429-35. doi: 10.4137/EBO.S12813. eCollection 2013.
PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.
Kocot KM1, Citarella MR, Moroz LL, Halanych KM.

Phylo-MCOA 1.4 – Analysis of large Samples of Phylogenetic Trees

Phylo-MCOA 1.4

:: DESCRIPTION

Phylo-MCOA (multiple co-inertia analysis) is a set of functions written in R for the analysis of large samples of phylogenetic trees. It allows the easy and fast identification of outlier genes and species.

::DEVELOPER

The Biometry and Evolutionary Biology laboratory (LBBE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 Phylo-MCOA

:: MORE INFORMATION

Citation

Mol Biol Evol. 2012 Jun;29(6):1587-98. doi: 10.1093/molbev/msr317. Epub 2012 Jan 3.
Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis.
de Vienne DM1, Ollier S, Aguileta G.

TreeGraph 2.15.0 – Graphical Editor for Phylogenetic Trees

TreeGraph 2.15.0

:: DESCRIPTION

TreeGraph is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

TreeGraph

:: MORE INFORMATION

Citation

Stöver B C, Müller K F
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
BMC Bioinformatics 2010, 11:7

TOPD/FMTS 4.6 – Comparing Phylogenetic Trees

TOPD/FMTS 4.6

:: DESCRIPTION

TOPD/FMTS  (TOPological Distance / From Multiple To Single)is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • tcl/tk
  • Perl

:: DOWNLOAD

 TOPD/FMTS

:: MORE INFORMATION

Citation

Puigbo P., Garcia-Vallve S. and McInerney J.O. (2007)
TOPD/FMTS: a new software to compare phylogenetic trees.
Bioinformatics, 23:1556-1558. doi: 10.1093/bioinformatics/btm135.

jsPhyloSVG 1.55 – Javascript Library for Visualizing Interactive & Vector-based Phylogenetic Trees

jsPhyloSVG 1.55

:: DESCRIPTION

jsPhyloSVG is an open-source javascript library specifically built for rendering highly-extensible, customizable phylogenetic trees. jsPhyloSVG can render complex trees, yet offers a simple method to do so. It leverages the recent XML schema definition specified for phylogenetic trees, phyloXML.

::DEVELOPER

jsPhyloSVG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

jsPhyloSVG

:: MORE INFORMATION

Citation

Smits SA, Ouverney CC, 2010
jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web.
PLoS ONE 5(8): e12267. doi:10.1371/journal.pone.0012267

iTOL 5.2 – Display & Manipulation of Phylogenetic Trees

iTOL 5.2

:: DESCRIPTION

iTOL (Interactive Tree Of Life) is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized trees (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser (Firefox)

:: DOWNLOAD

 iTOL

:: MORE INFORMATION

Citation

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Letunic I, Bork P.
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259. doi: 10.1093/nar/gkz239.

Bioinformatics. 2007 Jan 1;23(1):127-8. Epub 2006 Oct 18.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P.

Letunic I and Bork P (2011)
Nucleic Acids Res doi: 10.1093/nar/gkr201
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Exit mobile version