Hello Karthik According to my notes while going through this process, "Header lines in the FASTA files should not contain ':' or '-' to avoid parsing problems."
Also, I noted later in my notes that you should avoid "=" and "," (commas) in the contig names (header lines). Performing a dos2unix is always a good idea. If using Win7 for some of the text manipulations, installing CygWin (which includes dos2unix) will help you eliminate many text file formatting issues. Alternatively, the Windows software NotePad+ allows you to easily convert from Windows end-of-line (EOL) format to linux format. I hope that helps. Peter Hoyt Oklahoma State University On 11/14/2014 5:43 PM, Hullahalli, Karthik wrote: > Dear Support Group, > > I have aligned 78 Enterococcus faecalis genomes, and I am currently trying to > construct a phylogenetic tree based on the alignment file in XMFA format. > This alignment was done on a computer running Windows 7, and we have problems > that occur when we try to manipulate this file (specifically with > StripSubsetLCBs) on a different computer running a UNIX environment. > StripSubsetLCBs claims that the length of sequence described in the FASTA > header is different from the length of sequence that is actually read. > > For example, if the following was the input, > >> seq1:1-10 > AGTCGATCGA > > anything trying to read this file on the other computer would claim that the > length of the sequence was actually more than 10, even though actually > checking the file shows that the length is indeed correct. > > Is there any way to fix this issue, or any other way to attain a phylogenetic > tree from Mauve outputs? > > Regards, > Karthik Hullahalli > > ------------------------------------------------------------------------------ > Comprehensive Server Monitoring with Site24x7. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > Mauve-users mailing list > Mauve-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
