[Mauve-users] Number of Breakpoints

Hello, I read in the online manual, under *Computing a pairwise breakpoint distance matrix, *that "Prior to alignment, progressiveMauve attempts to compute a conservative estimate of the number of rearrangement breakpoints among any pair of genomes." Is it possible to obtain this number? Thanks,

[Mauve-users] Exporting ordered contigs

Hello, Is it possible to export the contigs in the order they mapped to the reference after using Contigs Mover? Thanks, Rajeh -- ___ Mauve-users mailing list Mauve-users@lists.

[Mauve-users] Mauve Contigu Mover Code

Hello, I’d like to look into the contig mover code and see if I can expand on it. The problem is I can’t really find it. Could you please help me locating it? I have the entire Mauve package setup in eclipse. Thanks, Rajeh

[Mauve-users] Mauve's Approach To Multiple Alignments

Hello, I have a question about Mauve’s algorithm: How does Mauve deal with contigs that are found in more than one region in the reference? I tried to test this by aligning a contig I had to a reference containing the same contig twice. Mauve only aligned the contig to the first occurrence in t

[Mauve-users] 2 Questions: LCB and Exporting Contigs With Multiple Alignments

Hello Mauve-users, I have 2 questions: First, could someone please explain seed weight and minimum LCB to me? The manual's descriptions are unclear to me. For example, all I want is to consider contigs that share at least 1 kb with the reference, with maximum 0.01% mismatch. How can I do that? Se

[Mauve-users] Fwd: Exporting Unmapped Regions/Contigs

Hello, I'm using Mauve to map assembled contigs of s.pombe back to the reference. I'm interested in studying regions that did not map back to the genome as they could be insertions in the genome of the assembled strain or deletions in the reference. The "Export Gaps" option only gives me the coor