Dear all, my RAXML run was interrupted after all bootstraps were completed. The RAXML specialists advice: "However, since you already have the bootstraps, you can now independently compute a couple of ML trees (see manual) and then use these results to do post-analyses ..." (https://groups.google.com/forum/?hl=en#!searchin/raxml/interrupted$20run%7Csort:date/raxml/BoFLQYrBlT8/pqLRqIgWxVYJ)
Unfortunately I cannot find the needed command in the manual. Can anybody, please, point me the right place or explain how to build the best-scoring ML tree and continue with the analysis if the raxml bootstrap file has been generated already?
thank you for the help in advance! :)