Hi Pilar,

Clustal is actually not a software for phylogenetic analyses, but for optimal alignment (which is of course crucial for the later analyses). MEGA is indeed a nice software for fast analyses. I often use it to get a first overview of my data. Later (if you want to publish a tree), you should use other methods, particularly Bayesian Inference is known to perform very well. You can use the programme MrBayes (but make sure that you find a good tutorial in the internet - it is not as self-explaining as MEGA).

Best wishes,

Axel

Hey Pilar,

have you tried out MEGA?

Very easy to use and covers many phylogenetic tools

-Ijad

http://www.megasoftware.net/

Hi Pilar,

Clustal is actually not a software for phylogenetic analyses, but for optimal alignment (which is of course crucial for the later analyses). MEGA is indeed a nice software for fast analyses. I often use it to get a first overview of my data. Later (if you want to publish a tree), you should use other methods, particularly Bayesian Inference is known to perform very well. You can use the programme MrBayes (but make sure that you find a good tutorial in the internet - it is not as self-explaining as MEGA).

Best wishes,

Axel

There is always PHYLIP - been a standard for phylogenetic inference for decades now.

http://evolution.genetics.washington.edu/phylip.html

In addition to MrBayes I'd suggest maximum likelihood analyses, e.g. with RAxML (http://sco.h-its.org/exelixis/software.html). If you don't want to bother with command line control, try the python-based graphical interface for it: raxmlGUI (https://sites.google.com/site/raxmlgui/)

Thank you very much to all. Very good suggestions that I will start trying

I will recomend Mega, phylip, Geneious etc

I think for the start it would be easier for you to use some web-based tools, then you can try different, select your favourite and later you can download them, if you feel a need for that.

You can try the website http://www.phylogeny.fr/. There you can find: 1. set of tools for multiple alignment, such as Muscle, T-Coffee, etc. Clustal is also there, but actually Clustal is not an optimal approach. I normally use Muscle. 2. Set of tools for building of phylogenetic trees. For fast trees you can use BioNJ (Neighbor Joining), but as this is a distance-based method, it is not the best way to go. It's good for a first look of if you need the trees "quick and dirty". For better results, go for PhyML, but remember it takes much more time. (you can also use PhyML here: http://www.atgc-montpellier.fr/phyml/, sometimes the server is faster here). MrBayes is even better approach, but in this very website it is restricted to only 30 sequences. If you have more sequences and want to use MrBayes, you have to download it or find another web application. 3. Finally, to see your tree you can use any of the tree viewers on the site. I like TreeDyn, because there you can interactively edit the tree.

There are other similar websites, e.g., Phylemon (http://phylemon.bioinfo.cipf.es/).

MEGA would be one of the choice as it's user-friendly and the analysis is faster.

It depends what you want to do and for what purpose; why do you need your tree? If you want to do phylogenetic analyses, you basically need programs on 3-4 stages. FIrst you need programs to handle your data; usually to align (Clustal, Muscle, Mafft) and then analyze the evolutionary models (jModeltest, MrModeltest etc). Then you analyze the data with the phylogenetic programs, but then you need to select which approach you use - a) parsimony (Phylip etc), b) maximum likelihood (RAxML, Garli etc), c) Bayesian (MrBayes). Then you need to sum your trees in some program and after that view and notate your trees eg. with FigTree.

In terms to tools Phylip is best, but not easy to use. I strongly prefer MEGA, its very easy to use and can do lot of analysis on one click and you can even save the session of your work. Its simply great. Great work by Dr. Kumar S

Hi Pilar,

You have pretty good suggestions from many people now. It is very good summary of different phylogenetic methods, however one possibility is still missing. If you would like to run alignment and phylogenetic analysis in one step, you can use the program POY (http://research.amnh.org/scicomp/scripts/download.php). The input sequences need not to be prealigned and it works under Maximum Parsimony, or under Maximum Likelihood. Nevertheless, I am not sure, if it is good for beginners, although it have very good manual.

Good luck,

Lenka

I think POY is very suitable for beginners, Lenka, as I was one of them and learned to use it (with that good manual) in one day.

Hi Pilar.

A nice introduction to phylogenetic analysis for a beginner is the book "Phylogenetic Trees Made Easy: A How-To Manual".

Best wishes

The journal of Methods in Ecology and Evolution recently published a list of free phylogenetics analysis software, You might want to check it out:

http://www.methodsinecologyandevolution.org/view/0/applicationpapers.html

Thank you very much to all of you, you have been a great help.

For a basic, clear and complete apprach to phylogeny I suggest you to start from MEGA5 (http://www.megasoftware.net/). It is user friendly, free download, and cited in scientific journals.

Good luck,

G.

Google for "seaview"

Download for your system (Linux, Mac or Windows)

No sudo install required, simply unpack and execute

Deals with aa or nucleic acid sequences

Reads many formats

If sequences are nucleic but protein coding, you can visualize/align sequences in either mode and go back and forth between the two modes !

Includes by default (parameters can be easily adjuster for each)

- manual align

- clustal align

- muscle align

- you can add other of your choice (mafft ?)

Note that for muscle, if you have too many sequences you have to adjust parameters to allow use more memory.

Once your sequences are aligned, you can easily select sites on which to compute a tree (or sequences and sites).

Compute a tree using

- neighbor joining

- phyml

- parsimony

Each highly configurable from the graphic interface

Visualize your tree, re-root , swap,... see sub-trees.

Once tree is computed and re-organized, you can re-organize sequences in the order of the tree; very convenient to manually refine your alignments...

Export as newick or pdf

Note that for dealing with resulting trees, I suggest TreeDyn, but this is a different story :-)

Best

http://evolution.genetics.washington.edu/phylip/software.html#methods

This link may help full for your question.Check it once.

Use BioEdit... http://www.mbio.ncsu.edu/bioedit/page2.html

Maybe Ugene is what you need http://ugene.unipro.ru/

http://bioinformatics.oxfordjournals.org/content/28/8/1166

You can use phylip programe and MeGA5 , and figtree is very easy.

Use Mr. Bayes and RaxML. Both are freely available. Very easy to operate.

how r u vikas ,how is ur life. how is ur kid. My regards to ur family

i agreed with Axel view that in phylogeny Clustal used only for alignment which is in built in MEGA and BIO-EDIT , so these two worked well for all aspect of phylogenetic analysis

MEGA and Bioedit are for simple analysis when you have few sequence, use simple algorithms (NNI, CNI etc.) but can be deceptive for complex questions, like phylogenetic inferences above species level, these can be used for quick outlook for beginners. Try heuristic search in MEGA for MP analysis, your system will hang for sure.

PAUP, Mr. bayes, RaxML, PhyML, etc. are good option which can give you robust and reliable results that are acceptable at any level. Though ML in PAUP is time consuming. Use modeltest in conjunction with PAUP or Jmodeltest is now available with GUI.

Since nobody has suggested it yet, I recommend TNT, a parsimony-based phylogenetic program which may be downloaded for free from http://www.cladistics.org/tnt.html

TNT does not rely on poorly-justified evolutionary models of character state transformation.

Use MrBayes to construct BI tree, RAxML to construct ML tree and PAUP to construct MP tree. These three kinds of trees are approved by the majority of phylogenetic biologists.

Pilar,

there are hundreds of nice and differently "friendly use" software and tools you can choose... I suggest you MEGA5 because it is simple and complete, from alignment to trees. Hope that helped,

G.

As Xianzhi Zhang said: If you believe in sequence-evolution models, and prefer Bayesian inference, use MrBayes; if Likelihood is your choice, there are several options (Paup, PhyML, MEGA, RAxML), RAxML is the fastest.

But if you want to do a parsimony analysis, then use TNT, a free software thousand of times faster than PAUP, and with many more options.

The size of the dataset could limit your choices: for parsimony, TNT can handle up to several thousands terminals; for likelihood, RAxML is the only option (MEGA is a real turtle here). Bayesian analisys is limited to hundreds of terminals on a single PC.

Mega

You will get one of the free softwares in the link: http://www.dna-software.co.uk/; nhttp://www.molbiosoft.de/; http://www.genepalette.org/GenePalette/Home.html; http://cobamide2.bio.pitt.edu/

Both MEGA and PHYLIP are equally good. PHYLIP takes longer to construct a tree but once you get hold over it, it is easier tooo. But if you are looking for tree construction of larger dataset, then definitely non of them will work for you.

I would recommend Mega in this case. It has good options to use. But remember to align sequences before constructing phylogenetic trees by Mega. Hope it helps

As most of relevant treatments are done by Maximum likelihood, I suggest GARLI, surely not the most friendly one but in my mind the best available free. I think that PAUP for most of analysis is staying anyway the reference.

reading all the posts.

I think that RAxML, GARLI are the best for ML, fully agree with Andrew (Brower) that TNT is very good for parsimony. PAUP is good for all.....but time consuming.

MrBayes and the derivated BEAST are....very dangerous, these software are not taking into account biological realities but only rough calculations. Many authors demonstrated that these tools (bayesian statistics for phylogenies) are not "really" valid. As regular reviewer for Molecular Phylogenetics and Evolution, I reject now all the papers with only this approach (I suggest to compare with a ML calculation most of time).

MEGA is easy but not accepted in most of high standard journals, therefore I can't recommand it.

Cheers from Mexico (actually in field trip there).

I am agree with Gian Maria Niccolò Benucci and Naurin

Pilar, I just cut and paste the information from the POY documentation. You can visit one of the program's download sites, where thera are the various versions available: http://research.amnh.org/scicomp/research/projects/invertebrate-zoology/poy?q=projects/poy.php

POY is a program that implements the direct optimization, fixed states, and search based alignment procedures of Wheeler (1996, 1999) as well as other character types. Although based on parsimony, POY can perform likelihood procedures.

Yeah MEGA is a very good software for initial analysis and to get an overview of how your data is behaving. You can do analysis such as p-distance calculation etc... You can also construct trees using MEGA, but thats it, they are not publishable, you cannot make any concrete conclusions from it.

Then you should use software like PAUP, RaxML, Mr. Bayes for building phylogenies.

Mr. Bayes uses bayesian inference, as the name suggests, the trees generated are quite good and reliable. And thats the future my friend.

Good luck

If you want a fairly decent all-in-one package then I would support the voices for MEGA, but if you'll be doing some more complex work I would go with RAxML or MrBayes/BEAST. The latter two are bayesian inference programs (as said by other people here) and take significantly longer to run, but are probably the future of phylogenetic inference (as also said by other people here).

I would recommend Mega version 5 but do alingment before phylogeny.You can also use phylip package, here boot straping is important.

You could start with MEGA,as already suggested. Use Mesquite, BioEdit and PhyDE for further phylogenetic studies. Sequence Matrix,RaxML, BEAST, TNT and MrBayes are also free!

For working on your trees, I recommend FigTree!

Cheers!

Jerome

I am surprised no one mentioned PHYML - it's well-tested and fast, reconstructs phylogenies using maximum likelihood based on different models: DNA, amino acids (many different ones) and includes a range of fast branch support methods:

http://www.atgc-montpellier.fr/phyml

Recently, we also developed a sister program CodonPhyML that allows to do the same inference but with a variety of codon models. This is useful if you are working with protein-coding genes. If so then try it out.

Download: http://sourceforge.net/projects/codonphyml/

Paper in Mol Biol Evol: http://mbe.oxfordjournals.org/content/30/6/1270

Good luck with your trees!

Just FYI,

there is a list of phylogenetic software on:

http://evolution.gs.washington.edu/phylip/software.html

Best regards, Peter.

MEGA is simply Good tool for Phylogenetic analysis of DNA or Proteins.

I use RAxML for ML analyses.

Mr. Bayes for BI analyses

BEAST for molecular dating BI analyses

*BEAST option in BEAST or BEST/Mr. Bayes for species trees (Can't

Started messing with Phylobayes for mixed models in a BI framework.

These programs avoid use of R or Python.

There are four things you should bear in mind:

1) what you are trying to do is essentially a statistical inference: we just don't know the history of life, so we try to make the best approximation from the data we have;

2) what you expect is a phylogenetic tree, which is a geometrical depiction of such history (a caricature if you wish) and has geometric properties that are relevant to compare it with similar trees;

3) you need to sort out what information is useful (i.e. phylogenetic signal) and what is basically noise (distorting that signal); and

4) beware of artifacts that are unavoidable and can be quite misleading.

Of course you are not expected to do this at once, but these points are most important when you are to decide what algortithm you want to use. So, distance-based methods such as NJ may be popular among microbiologists for example, but they are not phylogenetic inferences --just similarity clustering.

When using DNA data, a further issue is most relevant: given that you have only four possible character states (four possible nucleotides in each position), reversals are expected over time, thus confusing or even erasing the phylogenetic signal. That is why you need to have a model of evolutionary change.

So, here is what I woud recommend: use MODELTEST or a similar program to find out what model best fits your data. Then go to www.phylogeny.fr and paste your sequences there. It's very user-friendly, reliable, fast and free. Make sure you select the adequate evolutionary model. The default method is a powerful maximum-likelihood method --trust it. The tree you get can be shown in different ways. Then read about what the different steps of the process are, and get familiar with what the machine did. You will have a reasonable understanding and a robust tree. Afterwards you may decide to go deeper into phylogenetics.

Clustal W method is used to align multiple sequence .Phylogenetic and bootstrapping analyses could be carried out using DNASTAR Laser gene 8.1MegAlign program (DNASTAR, Inc). It is a simple program for beginners. Alternatively, if you are in a more advanced state you can use MODELTEST software, PAUP, and MEGA soft wares to create your phylogenetic trees.

Well - CLUSTAL is really just to be used for aligning sequences, which is necessary for the actual analysis procedure.

There are many different free programs to use to analyze sequence data and generate phylogenetic hypotheses.

MEGA is easy to use and may be a good first step for getting a sense of your data and the phylogeny generally speaking; however, I don't really care for the program as it is limited in its interface.

Perhaps the most robust phylogenetic software that is easily accessible and free would be MrBayes, which works in a Bayesian Inference framework. Of course, it is important to understand how these programs work in order to use them in a useful and informative way. This takes time and a lot of reading, as well as trial and error. Finding someone who knows how to do this work and can sit down with you at a computer will make your life much easier.

I think the disdain for Bayesian analyses seems unreasonable to me. There are papers that show that every sort of analysis fails in some situations. It is of course important to use different approaches to check for concordance among them, but there is a reason why so many people use MrBayes, and it is not because it is easy.