Hi Manal, On Tue, 2013-07-16 at 18:31 +0200, Manal Farid wrote: > how XFMA file can be converted to nexus or phylip for further > phylogenetic analysis > This can be done, but might require some scripting on your part. Each "block" in the XMFA file is an aligned segment. In principle these could be concatenated to a single very large alignment using a custom script and then used for phylogenetic analysis. Depending on which genomes you've aligned, it might make more sense to extract just the core genome using a program like stripSubsetLCBs first, and then create a concatenate of the core genome. See here for some brief instructions on using stripSubsetLCBs: http://code.google.com/p/clonalorigin/wiki/FromGenomeAssemblyToRecombination
I don't have any XMFA->phylip or nexus conversion tools but perhaps somebody else has created such a program? Note that there is an xmfa2maf tool, so if maf->phylip or nexus exists that might be a possibility. best, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
