Phylogenetic tree using genomes with Ns

Question

[sudheer.rvl]

Hi friends, I am doing a phylogenetic analysis using genomic fasta sequences for different strains of a virus. The fasta sequences have stretches of N nucleotide at several places in the genome. I have made phylogenetic tree using these sequences which included Ns. I shall be thankful if somebody suggest for following queries: Q1. Is it right to generate phylogenetic tree using genomes with several Ns ? Q2. Is there any method to exclude Ns from such phylogenetic study? Q3. Can we do same phylogenetic analysis using protein sequences from same genomes ?

Thanks in advance ...

[Joe]

A few more questions:

• What proportion of the bases in the genome are Ns?

• How long are the stretches of Ns? (Average/Range?)

• Do different genomes have N's in roughly the same places, or is it 'random'?

Also, can you elaborate about what you mean in Q3? You can perform phylogenetics with protein sequences or DNA sequences, but its not completely clear to me what you're asking.