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<BODY lang=RU style="tab-interval: 35.4pt" vLink=purple link=blue>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=312123816-04122002>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=312123816-04122002></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=312123816-04122002>Not
sure if I have an SUE, or reached a limit in the software or hardware. I
have a file with 457 fasta formatted sequences, that I want an MSF for, so I can
prettyplot it. I tried emma (see command line following). Can I use
a file of sequences, or do I need separate sequences, or have I broken the USA
formatting required? My file is like the example file, only with many more
sequences? The segmentation fault at the end concerns
me...</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><SPAN class=312123816-04122002><FONT face=Arial color=#0000ff
size=2>COMMAND LINE:</FONT></SPAN></DIV>
<DIV><SPAN class=312123816-04122002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>~/sequences $ emma -inseqs <SPAN
class=312123816-04122002>seqs</SPAN>.fa<BR>Multiple alignment program -
interface to ClustalW program<BR>Output sequence [1001501.aln]:<BR>Output file
[1001501.dnd]:<BR>..clustalw -infile=5511A -outfile=5511B -align -type=dna
-output=gcg -pwdnamatrix=iub -pwgapopen=10.000 -pwgapext=0.100 -newtree=5511C
-dnamatrix= -gapopen=10.000 -gapext=5.000 -gapdist=8 -hgapresidues=GPSNDQEKR
-maxdiv=30..</FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV><FONT face=Arial
color=#0000ff size=2>
<DIV><BR> CLUSTAL W (1.82) Multiple Sequence Alignments</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Sequence type explicitly set to DNA</DIV>
<DIV> </DIV>
<DIV>ERROR: Could not open sequence file 5511A</DIV>
<DIV> </DIV>
<DIV><BR>No. of seqs. read = -1. No alignment!<BR>Error: failed to open filename
5511B<BR>Problem writing out EMBOSS alignment fileSegmentation
fault<BR></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=312123816-04122002>-mat</SPAN></FONT></DIV>
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