I understand that multidna2genind is not part of mmod, but apex is no longer being maintained...so I thought perhaps you could advise me (as mmod relies on this function).
I am reading in fasta files from different genes from the same msa, but cannot for some reason build a genind object with them (see below). These are nucleotide alignments and their names have no "." in them.
Similary, if I try to build a genind object from a DNAbin object, I run into trouble (see below below).
Sorry to bother you with this, but any help would be appreciated.
als.gid<-multidna2genind(als,mlst=T,gapIsNA=T)
Error in .local(.Object, ...) :
more than one '.' in column names; please name column as [LOCUS].[ALLELE]
In addition: Warning messages:
1: In df2genind(xdfnum, ploidy = 1, ind.names = x@labels) :
character '.' detected in names of loci; replacing with '_'
2: In df2genind(xdfnum, ploidy = 1, ind.names = x@labels) :
entirely non-type individual(s) deleted
convert DNAbin to genind
al1<-read.FASTA(files[1])
al1
3535 DNA sequences in binary format stored in a list.
Hi,
I understand that multidna2genind is not part of mmod, but apex is no longer being maintained...so I thought perhaps you could advise me (as mmod relies on this function).
I am reading in fasta files from different genes from the same msa, but cannot for some reason build a genind object with them (see below). These are nucleotide alignments and their names have no "." in them.
Similary, if I try to build a genind object from a DNAbin object, I run into trouble (see below below).
Sorry to bother you with this, but any help would be appreciated.
read alignments
remove . from names
build genind object
convert DNAbin to genind
3535 DNA sequences in binary format stored in a list.
All sequences of same length: 225
Labels: X534418 X534419 X049951 X123292 X123293 X226610 ...
Base composition: a c g t 0.209 0.200 0.187 0.404 (Total: 795.38 kb)