Connect with us

Phylogenetics

Most widely used tools for phylogenetic tree customization

Dr. Muniba Faiza

Published

on

Most of the times, it is a very tedious job to convert file formats in bioinformatics, especially when we are dealing with phylogeny. Most of the available online servers mess your file and the output format is also not supported by the other programs. Additionally, it is quite difficult to perform other customizations on the phylogeny tree.

The basic requirement for using any bioinformatics software/tool is the file format and it is very difficult to deal with the phylogenetic tree conversions for the beginners sometimes. There are a bunch of tools available to visualize and annotate phylogenetic trees. Some of the most widely used software/tools are discussed below:

1. MEGA [1]

MEGA is a useful software in constructing phylogenies and visualizing them, and also for data conversion. It can easily convert alignment files to other formats such as nexus, paup, phylip, and fasta, and so on. The MEGA tree explorer is helpful in editing trees very easily, subtrees can also be selected and edited separately. Some tree image export options are also available. The input formats are newick, phylip, mega, and nexus. The phylogenetic tree can also be converted in newick format but it falls short on converting it into other formats such as phylip which is required in other analyses such as selection analysis.

2. Dendroscope [2]

It is helpful in visualizing large trees and provides several options to export their graphics with a command line. Several different views are also available, trees can be easily re-rooted and node labels and branches can be easily formatted. It can export trees in newick and nexus format. Although users will have to register themselves first to use this feature.

3. FigTree [3]

It is actually designed to visualize trees that are produced by BEAST [4] program. Tip labels and node labels can be easily edited. It can easily export trees in nexus, newick, and JSON format with some graphics export options such as emf, pdf, sg, png, etc.

4. Phylotree.js [5]

It is a javascript based library to visualize and annotate trees and offer some other customizations. It has a wide application in Datamonkey [6] comparative analyses. A user can upload trees using Phylotree.js where a user can easily select test and reference branches, and any changes can be mapped to their position on the corresponding structure. It is also good for comparison of trees with links between leaves known as a tanglegram, where crossings can represent evolutionary events. It also offers several export options and other built-in features [5].

5. ggtree [7]

ggtree is an R package for phylogenetic tree visualization and annotation. It also displays annotation data on the tree apart from visualizing it. Users can annotate trees with their own data and can easily convert trees into a data frame, and a lot of other features are available (https://guangchuangyu.github.io/software/ggtree/).

There is various other software available to visualize and customize phylogenetic trees such as NJplot [8], TreeGraph2 [9], and so on. We will be discussing their functional detail with examples in the upcoming articles.

References

  1. Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution33(7), 1870-1874.
  2. Huson, D. H., & Scornavacca, C. (2012). Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Systematic biology61(6), 1061-1067.
  3. http://tree.bio.ed.ac.uk/software/figtree/
  4. http://tree.bio.ed.ac.uk/software/beast/
  5. Shank, S. D., Weaver, S., & Pond, S. L. K. (2018). phylotree. js-a JavaScript library for application development and interactive data visualization in phylogenetics. BMC bioinformatics19(1), 276.
  6. Delport, W., Poon, A. F., Frost, S. D., & Kosakovsky Pond, S. L. (2010). Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics26(19), 2455-2457.
  7. Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution8(1), 28-36.
  8. Perrière, G. and Gouy, M. (1996) WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie78, 364-369.
  9. Stöver B C, Müller K F: TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 2010, 11:7

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Advertisement
Click to comment

You must be logged in to post a comment Login

Leave a Reply

Phylogenetics

How to find a best fit model using IQ-TREE?

Dr. Muniba Faiza

Published

on

How to find a best fit model using IQ-TREE?

Previously, we have provided an installation tutorial for IQ-TREE on Ubuntu. In this article, we are going to perform model selection for a dataset using the standalone tool of IQ-TREE. (more…)

Continue Reading

Phylogenetics

Installing TREE-PUZZLE on Ubuntu

Dr. Muniba Faiza

Published

on

Installing tree-puzzle on Ubuntu

TREE-PUZZLE is a software to reconstruct phylogenetic trees using the maximum likelihood method [1,2]. It requires sequence data as input and implements a fast search algorithm and quartet puzzling. It can process large datasets easily. In this article, we will install TREE-PUZZLE on Ubuntu. (more…)

Continue Reading

Phylogenetics

Tutorial: Constructing phylogenetic tree using MEGA7

Published

on

mega7

MEGAX is a bioinformatics software/tool used for phylogenetic tree construction. In this article, we will construct a maximum likelihood (ML) tree for a number of protein sequences using MEGA7 [1]. (more…)

Continue Reading

Phylogenetics

Update: A multi-epitope in silico vaccine candidate designed for Covid-19

Dr. Muniba Faiza

Published

on

covid19-vaccine

Covid19 has created a great threat to human health. As you are aware, in this coronavirus outbreak, Bioinformatics Review has created a group, BiR-nCov19 Drug Development Team, to work on finding prevention to this disease. This research group consists of researchers from all over the world. (more…)

Continue Reading

Phylogenetics

Phylogenetics analysis of SARS-CoV-2 spike glycoproteins

Dr. Muniba Faiza

Published

on

Phylogenetic Tree of Covid Corona Virus with other Species

A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China [1]. This virus belongs to the coronavirus family from which previous outbreaks have emerged (SARS and MERS). They have been a great threat to public health causing many deaths including  SARS-CoV-2. There is no proper treatment available to cure this coronavirus disease (covid19). Scientists and researchers are trying really hard to develop a drug or a vaccine or a proper way to cure covid19. (more…)

Continue Reading

Phylogenetics

Installing and executing ProtTest3 on Ubuntu

Dr. Muniba Faiza

Published

on

Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criteria: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. (more…)

Continue Reading

Phylogenetics

How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?

Dr. Muniba Faiza

Published

on

If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program [2] to calculate the dN/dS substitutions rate. Here is how you can do it. (more…)

Continue Reading

Phylogenetics

Why To Study Evolution?

Published

on

Understanding evolution is critical for understanding biology. As the preeminent scientist Theodosius Dobzhansky stated, “Nothing in biology makes sense except in the light of evolution.” Evolution is the only scientific explanation for the diversity of life. It explains the striking similarities among vastly different forms of life, the changes that occur within populations, and the development of new life forms. Excluding evolution from the science curricula or compromising its treatment deprives students of this fundamental and unifying scientific concept to explain the natural world. (more…)

Continue Reading

Phylogenetics

Molecular Evolutionary Genetic Analysis

Published

on

MEGA: Molecular Evolutionary Genetic Analysis
It is important to know the basic molecular relationship between two living organisms as one begins performing comparative studies for knowing the evolutionary aspects and for contributing to knowledge base. Several tools and soft ware have been introduced for meeting the task of such analysis. Each tool has different algorithm and method to perform molecular phylogeny. Examples include; ClustalW, Dendroscope, Hyphy, PAUP and Phylip etc. Among them is the most efficient tool, MEGA, Molecular evolutionary phylogenetic analysis which performs both sequence analysis and phylogenetic analysis in a very sophisticated manner.
(more…)

Continue Reading

Phylogenetics

Monogenea: An Easy Portfolio for Molecular Phylogenetics

Published

on

Estimation of present day diversity of organism and understanding their diversity forms new cornerstones of conservation biology, evolutionary biology and ecology. Maintaining the totality of all texa from past to present and classifying into groups reflect how they have changed over the period of times. Necessarily, phylogenetics and evolutionary study of a particular group help out in knowing pattern of occurrence and relationships between two distantly related class or families and their descendents. (more…)

Continue Reading

LATEST ISSUE

ADVERT