Core genome size and alignment

[moorembioinfo]

Hi Chad,

The snp.phylip file contains variant sites of all 'core' fragments, is it possible to extract the full alignment of fragments as a multifasta file per genome?

Thanks in advance for any comments on this!

[chadlaing]

Hi,

If you specify locusAlleles 1 in the config file, an output file named locus_alleles.fasta will be produced. This contains a per-locus output of all "core" fragments from each genome (if they exist) for each pan-genome fragment. A per-genome alignment file of all the core regions could be produced, but at this time is not.

-Chad

[moorembioinfo]

Thanks!