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 ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bes...{{dropped:15}} _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/