I am trying to use the phylipnew package.
I have the following sequences in phylip format:
4 15
C ATGGCCGGGA GGTT-
D ATGGCAGGGA GGTT-
A ATGGCCGGAA GGTTA
B ATGGCCGGTA GGGTA
produced by clustal.
I now input it into fdnadist and get this one out:
4
C 0.000000 0.083014 0.074877 0.174794
D 0.083014 0.000000 0.170786 0.310384
A 0.074877 0.170786 0.000000 0.155764
B 0.174794 0.310384 0.155764 0.000000
I next try to input this one into fneighbor:
alanine[15:54]:/projects/karin/phyliptest>
/site/bioinf/EMBOSS-6.0.1/bin/fneighbor
Phylogenies from distance matrix by N-J or UPGMA method
Phylip distance matrix file: a.fdnadist
Error: Distances file found -1 rows, expected 4
Error: Unable to read distances file 'a.fdnadist'
Phylip distance matrix file:
alanine[15:54]:/projects/karin/phyliptest>
I get the same thing when I try to input the file from the examples on the
webpage for fneighbor:
alanine[16:02]:/projects/karin/phyliptest> cat embosstest.dat
7
Bovine 0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905
Mouse 1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629
Gibbon 1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583
Orang 1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710
Gorilla 1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083
Chimp 1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692
Human 1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000
alanine[16:02]:/projects/karin/phyliptest>
/site/bioinf/EMBOSS-6.0.1/bin/fneighbor
Phylogenies from distance matrix by N-J or UPGMA method
Phylip distance matrix file: embosstest.dat
Error: Distances file found -1 rows, expected 7
Error: Unable to read distances file 'embosstest.dat'
Phylip distance matrix file:
Error: Distances file is required
Died: fneighbor terminated: Bad value for '-datafile' and no more retries
alanine[16:02]:/projects/karin/phyliptest>
What am I doing wrong here? Have I misunderstood things completely?
Thanks!
Karin
--
Karin Lagesen, Ph.D.
[email protected]
http://folk.uio.no/karinlag
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