Can I infer phylogenetic relations with partial and whole genomes of an organism?

Question

[chrismanuel1993]

I'm trying to draw a phylogenetic tree for a type of virus. (Human Papillomavirus) So far I have some whole genome sequences and some that only spans one or two genes.

Although there are overlaps in these sequences, can I use them as is to do the phylogenetic analysis ? If not what options do I have ?

Answer 1

[Joseph Hughes]

Yes, you could use both partial and complete genomes in a phylogenetic analysis but the amount of missing data could potentially cause phylogenetic bias. The effect of missing data on phylogenies is still poorly understood and frequently debated. For more details on the impact of missing data, you may want to read some of the posts over on phylobabble.org: https://www.phylobabble.org/t/lets-quantify-the-impact-of-missing-data/72/12