Greetings aligners, I’ve recently completed the assembly of two insect genomes of ~350MB size. The contain repeat and noncoding DNA structure more similar to mammals than, say, drosophila. They are also about 5 million years divergent. Using progressiveMauve with default settings seems to have worked well for some of our downstream analysis but I am trying to improve the results if possible. I searched through the original publication and looked at this lists archives but was unable to figure out how changing some of the parameters might improve things. Are there any recommended settings for island-size, seed-family, hmm parameters, repeat penalty, or gap parameters, or others for large vertebrate-like genomes?
Also, what approach would you take to parse out statistics like number of rearrangements? progressiveMauve and all analysis are being carried out from the command line. Best regards, Jason Jason Hill, Ph.D. Wheat Lab Zoologiska Institutionen Stockholms Universitet D-419 Svante Arrhenius v 18B S-10691 Stockholm Sweden tel: +46 72 748 80 90
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