Hi all,
I am trying to analyze my two outbreak cases first by (ape) and (adegenet) to
check the phylogeny. When I analyzed them one by one, everything went on well.
However, when I combined these two cases together, I got stuck. Please see the
details as follow:
> dna <- fasta2DNAbin("F:/....../......../........./Transmission-SNPs.fasta",
> chunkSize=14)
Converting FASTA alignment into a DNAbin object...
Finding the size of a single genome...
genome size is: 42,701 nucleotides
( 2 lines per genome )
Importing sequences...
..............
Forming final object...
...done.
> dna
14 DNA sequences in binary format stored in a matrix.
All sequences of same length: 42701
Labels: 122992F-180929J_S3 125582R_206049B 179690I_S3 186712J_S11 188050C_S2
190156Y_S6 ...
Base composition:
a c g t
0.246 0.254 0.260 0.241
> D <- dist.dna(dna, model="N")
> hist(D, col="royalblue", nclass=14,
+ main="Distribution of pairwise genetic distances",
+ xlab="Number of differing nucleotides")
> snps <- seg.sites(dna)
> head(snps)
[1] 1 2 3 4 5 6
> length(snps)
[1] 42701
> D.tn93 <- dist.dna(dna, model="TN93")
> tre <- nj(D.tn93)
Error in nj(D.tn93) :
missing values are not allowed in the distance matrix
Consider using njs()
> tre <- njs(D.tn93)
Error in njs(D.tn93) :
distance information insufficient to construct a tree, cannot calculate
agglomeration criterion
I'm not sure what caused this error. In the analysis, I only used snps as the
DNA input.
Any suggestions?
Thank you very much in advance!
Kai
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