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<DIV><FONT face=Arial size=2>Hi all,</FONT></DIV>
<DIV><FONT face=Arial size=2>I am analyzing EMBASSY programs. I have to
construct a phylogenetic tree starting from a multiple alignment of DNA
sequences. I have performed a bootstrap simulation by means of
"eseqboot" program. The output is constituted of 100 resamples of the initial
multialignment. At this point I want to calculate distance matrices on each
bootstrap simulation using "ednadist" program, then I have to use "eneighbor"
and finally "econsense" to calculate the consensus tree.</FONT></DIV>
<DIV><FONT face=Arial size=2>Nonetheless, when I try to use the output of
eseqboot as input for ednadist (as suggested in the seqboot documentation
"<EM>... </EM><EM>you would run SEQBOOT,then run
DNADIST using the output of SEQBOOT as its input, then
run NEIGHBOR using the output of DNADIST as its input, and then run
CONSENSE using the tree file from NEIGHBOR as its input"</EM>), it returns
a warning:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>> ednadist eseqboot.outfile<BR>Nucleic acid
sequence Distance Matrix program<BR><FONT color=#ff0000>Warning: seqReadPhylip
14 sequences partly read at end<BR></FONT>Output file
[ednadist.outfile]:<BR>Distance methods<BR> Kimura : Kimura
2-parameter distance<BR> JinNei : Jin and Nei
distance<BR> ML : Maximum Likelihood
distance<BR> Jukes : Jukes-Cantor distance<BR>Choose the
method to use [Kimura]:<BR>Transition/transversion ratio [2.0]:<BR>Form of
distance matrix<BR> S :
Square<BR> L :
Lower-triangular<BR>Form [S]:<BR>Kimura</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>What does this warning mean?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>The output file contains only one distance matrix.
My goal is to obtain a file containing 100 distance matrices, one for each
bootstrap resample; is it possible? Could be a limitation of the ednadist
algotithm?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Regards</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Graziano</DIV>
<DIV><BR></DIV></FONT></BODY></HTML>