Have a look to PopArt:

http://popart.otago.ac.nz/index.shtml

Http://darwin.uvigo.es/software/tcs.html

http://www.fluxus-engineering.com/sharenet.htm

For maximum parsimony, you can use TCS (http://darwin.uvigo.es/software/tcs.html). For median-joining you can use NETWORK (http://www.fluxus-engineering.com/sharenet.htm). There is also HAPVIEWER (http://www.cibiv.at/~%20greg/haploviewer).

To convert fasta files to rdf, you can use DnaSp (http://www.ub.edu/dnasp/).

Cheers

Ferruccio

Thanks all

Does anyone know what the error means (in Network 4.6)

: The data file contains less than 3 different sequence? I don´t understand, because all my sequences are different.

@Karin, are you using only 3 sequence to run Network? If so, then maybe software not able to run 3 sequences only and you see the "error", i think. i also saw the same message if software can't run or not proper format of file etc. So, my suggestion is, you can add some more sequence from GenBank and see how Network works. thanks

P.S: for different sequence, i don't think its a problem (although i haven't check with different sequence from different species in Network, i did work from same species).

Have a look to PopArt:

http://popart.otago.ac.nz/index.shtml

PopART is great. There are a number of different network options available as well as the option to geotag your data and represent your network on a map. It's free and easy to use however when you create your nexus files ensure that everything is correct otherwise it won't work.

PopART took some time for me to get to work properly, and it's still in development, but I think it is a very good program and the author has been helpful with trouble-shooting issues. 

I find POPART more convenient than NETWORK (which is the program I use, based on the results of the simulation studies by Woolley et al 2008 in PLOS ONE 3(4):e1913), because the input / output formats are more flexible and straightforward. In particular, NETWORK outputs a raster of your network, while POPART allows you to save in vector formats (e.g. SVG or PDF), which you can edit in Illustrator. 

I found PopArt very interesting, but I would like to use more than a sequence block in the nexus file deriving from two different regions in the cpDNA. Is that possible? 

I wonder if it's possible to import aligned sequences in FASTA format in Network without using the commercial program DNA Alignment. Suggestions?

I use DNAsp, to export as a Roehl format, which is compatible with Network.

If you are familiar with R, you could use the 'parsimnet' function in the package haplotypes. http://cran.r-project.org/web/packages/haplotypes/index.html

Perhaps convert the fasta file to .meg format on Mega and then upload it to dnasp which offers an option of converting to rdf 

how to give colrs in haploview anyone pls tell me....

i am not getting good representation of network as like haploview pls tell me....

I need help because popart not recognize my sites to make a network of colors, I get everything black....

hello I didnt understand how in POPART  to make geotag file.I have aligned sequence fasta file which it accepts. also its not accepting my nexus file as i want to generate MP ancestral network

Try to use as a guide the nexus example file that is provided in the website documentation section.

thanks all

you can use DNAsp to get haplotypes, at the end of  haplotype file make a new nexus matrix with  location vs haplotypes, how many individuals are present in each matrix combination, then  you can open this in popart

Hi, may anyone tell me, what is wrong with my Popart or OS (windows 7, 64bit).  I can not input any file, even example. And cannot use "help" or assistant. There is an error window "error reading collection file 'c\users\...\appdata\local/trolltech/assistant\qthelpcollection_4.8.qhc: cannot load sqlite database"

The Pegas package in R is another option.

I have previously used DnaSP -> NEXUS file -> PopART which produced high quality outputs and the ability to move the network and placed in a way you so desire.

Recently I've started using R as it is a far more efficient means to create haplotype networks. However, the outputs seem to be of very low quality. Does anybody have a way to solve this?

Hi I want to generate a phylogenetic tree for the mitochondrial haplogroups from the excel data is there any free software for the generation of phylogenetic tree.

please help me thanks

Hi @Sadia Idress, you can try with ape package in R.

Yes you can use DNAsp to get haplotypes, and save as file in rdf format and open in Network 5.0 then draw network

you can use MEGA 7 for the construction of Phylogenetic tree

thanks Farah Naz

Do I need to align my data separately after phasing in DnaSP before using it as an input in Popart?

I used HapStar tool to generate the MS network, it use the output of Arlequin software for haplotype connection length.

PopART is recommended to create haplotype network after phasing using dnaSP. Here is a graphical guide to PopART,

http://blog.sciencenet.cn/blog-460481-1191502.html

Yes PopART is most useful for creating halpotype network in which there is need to use NEXUS file which can be derived from dnaSP software. Also some other softwares like MEGA for phylogenetic tree construction can be used. Also TCS and HapStar can be used for haplotype network.

http://popart.otago.ac.nz/downloads.shtml

http://popart.otago.ac.nz/

popart is most easy to create a haplotype network...input files are phylip,Nex. and there are many options of editing of network too......network 5.0, hapveiw are some other options for haplotype network..

you can convert a fasta file into a rdf format by using DnaSP software . load your file and generate a haplotype file nd there is a option of saving in rdf format...

Hello,

I was looking today for a software for the construction of mitochondrial haplotype network,

I propose this one: https://www.fluxus-engineering.com/sharenet.htm

But I am looking for a manual which will allow me to facilitate the task of the construction?

I will be delighted if I will find it here

Sincerely

For haplotype network drawing, Popart or network can be used. The Dnasp can be used to convert the fasta file into RDF format which then can be transferred to Network software for Haplotype network construction.

PopArt works well for small datasets, however for larger ones (>1000 sequences and ~15K + bp), it lags and essentially terminates itself. Best to find a unix-based program for bigger stuff. Barcode data though is easily processed by PopArt.

TCS is another good one (Java-based).