Question: Missing data in matrix- need help with Neighbor Joining
0
gravatar for ehamel00
5 weeks ago by
ehamel000
ehamel000 wrote:

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!!

software error • 97 views
ADD COMMENTlink modified 5 weeks ago by h.mon29k • written 5 weeks ago by ehamel000
1

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.

ADD REPLYlink written 5 weeks ago by JC9.6k

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.

ADD REPLYlink written 5 weeks ago by ehamel000
1
gravatar for h.mon
5 weeks ago by
h.mon29k
Brazil
h.mon29k wrote:

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

ADD COMMENTlink written 5 weeks ago by h.mon29k
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