Hi,I'm planning to run an alignment of a mix of bacterial genomes, some finished and some in draft status. I've tried the Mauve Contig Mover and it works well from command-line (running on linux). The question I have is related to choosing the "best" reference genome for each draft genome when ordering contigs. I have a phylogenetic tree based on a rather large set of single-copy orthologous genes present in all the genomes (obtained from the OrthoMCL program). My first idea was to choose the nearest neighbour in that tree with a finished genome. Then I started thinking maybe that doesn't tell me which reference genome is the best choice.
What I'm wondering is if the distance matrix that Mauve prints to the log is a good way of finding the best reference, i.e. for each draft genome choose reference genome with the smallest distance to the draft in the matrix.
Any help or guidance is appreciated. Thanks, John
------------------------------------------------------------------------------ Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d
_______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
