Hi Yunzeng, On Sat, 2014-05-31 at 01:54 +1000, Zhang,Yunzeng wrote: > Hi All, > > I used progressiveMAUVE to align my 25 bacterial genomes (each of them > has multiple fasta files), and got xmfa, bbcols and backbone file. > However, when I used stripSubsetLCB to extract subblocks, use > command ./stripSubsetLCB xmfa bbcols output.xmfa 5000 25, and I truly > got the output file and report that how many blocks were kept. > However, when I checked, the sequences in the output file were > unaligned, but I am sure the sequences in the original one were > aligned. That means stripsubsetlcbs did something wrong. Does someone > faced this problem? Any help is appreciated . BTW, my systems is > Linux 2.6.18-348.1.1.el5. > stripSubsetLCBs should never produce unaligned output. Can you send me (off-list) the input xmfa, bbcols, and output xmfa via dropbox or some file sharing service so I can have a closer look?
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