Which Genome Synteny Program?

Question

[jomaco]

Hi,

I'm interested in producing an image similar to figure 1 in this paper: http://www.nature.com/nature/journal/v461/n7262/full/nature08358.html#a2

Can anyone identify the program which may have been used to make this, or a program capable of producing a very similar image?

Although I have found a number of programs, I am not sure if any of them are capable of producing a publication quality figure.

Thanks,

Jom

Answer 1

[Neilfws]

From the acknowledgements section of that paper:

We thank [...] J. Crabtree for providing a Sybil (http://sybil.sf.net) software component used to render genome comparison illustrations

Link to software.

Answer 2

[Zev.Kronenberg]

my pipeline is: running lastz -> circos.

[chitoboy]

Hi Zev,

I am using the USCS Lastz pipeline, however, I would now like to visualize my MAF file on circos. Do you have a pipeline on how to visualize the multiple alignment file on Circos? Please let me know. Thank you

[Zev.Kronenberg]

I just re-format the tabular output option of lastZ into the link format for circos.

Answer 3

[Vitis]

Gbrowse_syn could do something similar, but you need to run the whole genome alignment first, which is usually not a trivial task. You could read the 'A Note on Whole Genome Alignments' section at the end of Gbrowse_syn webpage to give it a try. http://www.gmod.org/wiki/GBrowse_syn_Tutorial

Answer 4

[gammyknee]

Isnt exactly the same as that figure but ACT (https://www.sanger.ac.uk/resources/software/act/) will do something fairly similar

Answer 5

[cts]

EasyFig can make this sort of image