MEGA is a great program and Sudhir Kumar who has been working on it for many years really know his stuff. It has been cited several thousand times, it is free, it carries out most of the standard phylogenetic analyses and also interacts with internet resources. It is indeed a fine program. There are some other, more specialist programs out there that you might want for particular kinds of analysis, but for sure MEGA5 is a pretty fine program.

Hey Buhara,

I used MEGA in one of my papers in a phylogenetic study. Why do you ask? Is there anything wrong with MEGA?

-Ijad

nothing wrong. I wanna see how touched the isssues relavent to the statisctis, citations etc with MEGA only. I am a begineer in this research, started with MEGA. It seems very nice program. Could you send me your article if there is no mind to see the details about MEGA analyisis etc.?

The article is in my profile:

http://www.researchgate.net/publication/6311037_Phylogenetic_analysis_and_structural_predictions_of_human_adenovirus_penton_proteins_as_a_basis_for_tissue-specific_adenovirus_vector_design

Article Phylogenetic Analysis and Structural Predictions of Human Ad...

We've used MEGA in our publication in Mycologia (Mycologia July/August 2011 vol. 103 no. 4 806-819). The authors of the software are highly regarded in the field, and will actually respond to inquiries if you're wondering about a particular analysis. It's also the software that's recommended in the 3rd and 4th editions of "Phylogenetic Trees made Easy," a very nice handbook. Also, MEGA5 is free!

I would have no objections using MEGA. I have never heard anything against it.

MEGA is a great program and Sudhir Kumar who has been working on it for many years really know his stuff. It has been cited several thousand times, it is free, it carries out most of the standard phylogenetic analyses and also interacts with internet resources. It is indeed a fine program. There are some other, more specialist programs out there that you might want for particular kinds of analysis, but for sure MEGA5 is a pretty fine program.

i found MEGA to be a very good tool for phylogenetic analysis and its also user friendly.

MEGA is one of the easy quite complete tool that exists for phylogeny. it includes a lot of different methods and a tree editor that makes life much easier for phylogeneticians! I used it in at least 4 or 5 papers.

Just to be clear: MEGA 5 does in fact perform model-based maximum likelihood analyses. Not every kind of likelihood analysis, but it does perform ML analyses.

Mega is a commonly used software for phylogenetic analysis. You can have an idea about its application from the citation of each version of the software.

Mega 4: cited 14703 times

Mega 3: cited 10465 times

Mega 2: cited 8166 times and

Mega: cited 908 times

You can use it comfortably.

MEGA is simple to use and user friendly phylogenetic tool. one can find n numbers of good papers where MEGA has been used. One example can be find using following link: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001234

Yeh! Correct, MEGA is one of the widely used s/w for application in genetic diversity studies and phylogeney tree construction.It is equally important for many others aspects of genetics like analyzing mutations, translational of nucleic acid sequences to amino acid sequence and many more......

Yes I normally used MEGA5 to calculate the sequence divergence in my study.

I am not an expert in phylogenetics by any means, however, for the sequence analyses in which I have been involved, it has proven to be very effective. Attractive features from my perspective include: the colourful and convenient manner in which it handles sequence alignments, allowing for very easy manual editing, flipping between DNA and AA sequences, and sequence by sequence reverse complementing i.e. you can reverse complement a single sequence in a larger aligned group, leaving the others in the same orientation. It's very format friendly, allowing easy import/export in various formats, and handle various types of phylogenetic analyses and tree construction/editing with ease. As others have indicated, it is widely used/cited by the scientific community. I have successfully used it in publications, and will continue to do so, currently working with versin 5.

MEGA5 is very common tool software for constructing some phylogenetic relationship of bio (eg, insect) , I found many articles related to genetic analysis mentioned this software

MEGA is generally very popular software, widely used, and user-friendly. Another popular tool will be PHYLIP

Hi, all. I would like to construct phylogenetic trees using PAUP, PhyML, and Mrbayes.

HI, MEGA is one of the most common softwares, friendly and easy to use

I think the above comments say it all - MEGA 5 is great, that along with MrBayes and Phylip covers most needs. You can do NJ, ML, parsimony and minimum evolution type trees. Also with regards to MEGA 5 - you get an alignment tool, alignment editor, dN/dS calculator, a find best model program for ML analysis etc. also you can use it as a "data mining tool" similar to DAMBE by downloading sequences via various blast options. Overall MEGA is a "must have" package.

Have you tried searching via Google Scholar for the publication by Tamura et al. 2011 ("MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods") and then using the "cited by" option? By this, you should get plenty of good articles citing MEGA.

MEGA is nice software for preliminary phylogenetic analyses. I like it very much.

MEGA is good software . Can combined phylogeny of different coding and non-coding genes be used to make a single phylogenetic tree in MEGA?

Thank you Shrestha. As far as I know, you cannot combine different trees based on different genes, but you can do that manually.

Thanks alot Yucesan I have heard about Nexus file format for same work in PAUP, can't it be used in MEGA as well?

Mega is a very reliable phylogenetic program which can allow you to perform many analyses. It is very convenient and compatible with other software. Also there are many researchers who are using the software or have published their works based on the program so all in all it is one of the best free programs to go for in phylogeny.

I would also recommend the BEAST if you are attempting to perform bayesian analyses on your data.

Dear Jagat Chhipi Shrestha

if you are referring to using a nexus format in Mega, in Mega 5 you are provided with the option of opening the *.nex file in the program and then convert it into a *.meg extension and work with on it. Just remember to check the converted file as there might be unwanted changes. So checking comes first. But it usually works very well.

Is it possiable to create file in nexus format with MEGA 5 program? Thanks.

Hi Natalya,

I'm not sure about Mega 5. But if you intend to change formats (from any to any, e.g. Fasta to Nexus) use this online link. Works pretty well:

birc.au.dk/software/fabox

Cheers