Reference-free package for comparative genomics

Software and scripts to run the Reference-Free Comparative Genomics pipeline at Sourceforge:

Get the package!

You can stream tutorials for running the Reference-Free pipeline at the following links.

Tip pipeline

Group pipeline

A proof-of-concept analysis of 174 chloroplast genomes can be downloaded from PLoS One:

Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11): e48995. doi:10.1371/journal.pone.0048995 site