areagp61 at yahoo.it
Wed Apr 30 11:19:21 UTC 2003
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.
Nonetheless, when I try to use the output of eseqboot as input for ednadist (as suggested in the seqboot documentation "... 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"), it returns a warning:
> ednadist eseqboot.outfile
Nucleic acid sequence Distance Matrix program
Warning: seqReadPhylip 14 sequences partly read at end
Output file [ednadist.outfile]:
Kimura : Kimura 2-parameter distance
JinNei : Jin and Nei distance
ML : Maximum Likelihood distance
Jukes : Jukes-Cantor distance
Choose the method to use [Kimura]:
Transition/transversion ratio [2.0]:
Form of distance matrix
S : Square
L : Lower-triangular
What does this warning mean?
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?
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