Missing data in matrix- need help with Neighbor Joining

Question

[ehamel00]

Hi all,

I have an FastME NJ error. I have a matrix where the distance between two of the taxa is unknown. So far, none of the NJ versions can seem to handle this. I tried FastME and BioNJ. Please help!!

[JC]

I have a matrix where the distance between two of the taxa is unknown.

Your matrix is not good, you need to have a distance for all your pairs.

[ehamel00]

I got the matrix from 25 fasta files. One file represented one gene. There was no file that had both taxa 14 and taxa 7, hence the missing data. I am not sure how to account for that case.

Answer 1

[h.mon]

Try DAMBE, which implements a method to impute missing distances.