PopGenome Not Reading In FASTA File
I'm trying to run my alignment of a gene (CDS) with multiple species and multiple individuals per species. When using the 'readData()' function in the PopGenome package, I can see that it's reading in my file because it shows the correct number of sites, but doesn't show anything else (# gaps, unknowns, trans/transv ratio, etc).
> get.sum.data(Croc_AVP.class)
n.sites n.biallelic.sites n.gaps n.unknowns n.valid.sites n.polyallelic.sites trans.transv.ratio
ExonCap-Crocodylus_AVP_outNT_MKTtest.fasta 858 0 0 0 0 0 NaN
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Popgenome nvalid sites
written by shinken123
Could your fasta file have Microsoft style linebreaks instead of proper *nix linebreaks?
I thought about that when comparing my file to their example file! I'm on Unix but my collaborator could have been using Windows. How could I "convert" the file if that's the issue?