Comments (1)
There is no need to specify an outgroup, this feature just places that sample at the start of the alignment (since many phylogenetic programs will "root" the tree at the first sample). If you want midpoint you will have to provide an option to your phylogenetic software.
Edgardo
from vcf2phylip.
Related Issues (20)
- Hours taken to find the ploidy HOT 9
- Give option for name and directory of output file HOT 3
- Installation problem HOT 3
- transfer vcf file of SV into phylip failed HOT 5
- Invalid character * in the alignment HOT 10
- Coordinates of alignment sites HOT 2
- UnboundLocalError: local variable 'used_sites' referenced before assignment HOT 3
- Max character length for seq IDs HOT 2
- output path issue HOT 6
- error HOT 1
- ImportError: No module named pathlib HOT 2
- Can't regonized by Treebest to buid NJ tree
- All of the SNPs were removed by vcf2phylip HOT 3
- SNPs that passed the filters: 0 HOT 5
- All SNPs were removed by vcf2phylip HOT 3
- error: unexpected end-of-file. HOT 2
- unexpected token 'newline' error HOT 2
- KeyError: '2': always met this error when converting a vcf file to phylip file. HOT 5
- issues convert vcf file to phylyp HOT 9
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from vcf2phylip.