The only one I know of is TCS http://darwin.uvigo.es/software/tcs.html. You have to modify it after for labels colour etc. but it can generate a simple schematic haplotype network.

You can use Network software package: http://www.fluxus-engineering.com/sharenet.htm

These both work for the analysis, but do not help with the drawing part. Any ideas on the best approach for turning the output of TCS, for example (which I have used), into a usable and attractive figure?

I use ADOBE illustrator for all my drawing and figure modifications. You could probably also use power point though the output formats are more limited.

I use Inkscape - a vector graphical, open source programme. http://inkscape.org/

Otherwise, Network can draw you very nice figures, for example: http://www.nature.com/jhg/journal/v55/n4/fig_tab/jhg20108f2.html

http://www.sciencedirect.com/science/article/pii/S1055790311004866

But as I remember, you have to pay for the better quality drawing software.

I prefer Adobe Illustrator; Excel-cake pies can be also visualized if you copy and paste them.

Seems like Adobe illustrator is the preferred choice for the drawing component. Shame that it is so expensive.

Inkscape should do almost everything Illustrator does and is free and open-source.

I also recommend Inkscape. A network/graph alternative is Graphviz, which will visualize the tree if you give it the connections in a very simple text file. It will produce output in a variety of graphic formats. I've drawn very large and complex networks (food webs) by manipulating GraphViz files to highlight or differentially colour various components, e.g. species, links, and then combined them in the Gimp using layers.

I also use Network. How do you take the output of network and use it to create a figure in Inkscape or Graphviz? I can only export poor quality .bmp files with Network. Do you just trace over this?

You cannot import graphics into Graphviz. Instead you give it a text file which outlines the nodes and links, and it does the rest. I think that you can import bmp bitmaps into Inkscape though.

Thanks Peter. Can you output the necessary text file from Network? I appreciate the help!

Not sure Sean, since I haven't used Network before. But the Graphviz format is pretty simple. Check out their website for lots of examples.

Thanks Peter. Anyone with experience in Network, I would greatly appreciate reading your experience.

TCS and NETWORK, both are used and accepted. Use of NETWORK software for phylogenetic analysis is bit tricky, but at the same time much informative than using TCS. If you could tell me your sample size i might help you further in using NETWORK

Normally I will draw it manually by using CorelDraw, but now I am using NETWORK too after I found that it can actually giving the same set of result. You can export the graphic to .pdf format and edit it.

This program might also be useful- creates very clean graphs: http://fo.am/hapstar/

Thanks for sharing, Hoban.

One year after this question, do we know about a program/script (R, python) to perfom pie charts (based on species/geography/phenotype/whatever) without doing it manually (time consuming) or pay an expensive price for network publisher ($800 for undefinite lease), using the network output? Thanks.

Cytoscape: http://apps.cytoscape.org/apps/igraphplugin

I've found an interesting software, developed by Jessica W. Leigh: popART (http://popart.otago.ac.nz/index.shtml).

Thanks for all of these comments, and apologies that I did not get back with feedback on the outcome for the questioner! I used TCS in the end (ver 1.2.1) which was free, and did the drawing in Powerpoint, which was a bit tedious, but worked well enough. Probably Inkscape would be better for this, but there is a learning curve which I decided not to get into. For anyone interested, here is the paper. Cheers for all your great ideas and suggestions. If I need to do the same again, I will definitely revisit this discussion. Thx

This is an old thread, but if you come across this problem again. You can use the 'parsimnet' function in the R package haplotypes. This gives single statistical parsimony network (without loops). Generally it is the most parsimonious network . If algorithm finds more than one best network, only the minimum spanning network is returned.  Graphical representation is  better than TCS but you still need a program like Inkscape or Illustrator for better graphics.  http://cran.r-project.org/web/packages/haplotypes/index.html

Very useful thank, Caner. I will check it out next time I need to do this sort of thing. Thanks for the input in spite of this being a VERY old thread!

My pleasure, feel free to ask further questions.

Use PopART. This nice program allows you to draw networks with various algorithms (e.g. Median joining, Minimum spanning, TCS and others not so well known) and edit them. PopART reads NEXUS-format alignments. Don't forget to create the TRAITS block (and GeoTags block if you want) in your NEXUS-format input files.

Can anyone comment on the Network Publisher add-on? Have any of you purchased it and would you please comment on the ease of use, worth the license investment, etc? I am looking to purchase the one year license for a non-commercial lab site ($145). Thank you!

Use of inkscape software might be helpful in this regard.

It is free vector graphics software available for multiple platform where you can edit any kind of vector graphics content