Hi fellas, One workaround is to convert the xmfa output to MAF and then in Galaxy get a fasta alignment. Although I think it would make more sense to get some sort of core genome using StripSubsetLCBs first and then create a file for partitioned analysis.
Hope it helps Eduardo On Jul 17, 2013, at 1:33 AM, Aaron Darling <[email protected]> wrote: > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
