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.
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