[EMBOSS] Segmentation fault with multiple similarity matricies in fdnadist

[Peter Rice]

dear hazel,

Hazel Hartman Jenkins wrote:

> If I run the following command;
> fneighbor -datafile tinytest.dat -replicates y -outfile filefrom.fnb
> then everything works.
> 
> If, however, my tinytest.phy contains two  similarity matricies (or, for 
> that matter, the one hundred bootstrap replicates written by fdnadist by 
> default), like this;
>     3
> 1187Aquife  0.000000  0.368385  0.404489
> BB213b06    0.368385  0.000000  0.151182
> BB269b06    0.404489  0.151182  0.000000
>     3
> 1187Aquife  0.000000  0.368385  0.404489
> BB213b06    0.368385  0.000000  0.151182
> BB269b06    0.404489  0.151182  0.000000
> 
> then fdnadist returns;
> <quote>
> Phylogenies from distance matrix by N-J or UPGMA method
> Segmentation fault
> <endquote>

Ah, firstly that is a bug in reading distance matrices. The reading should stop 
after the first 3 rows of data. That is easy to fix.

I will look into handling multiple distance matrices in one file ... there seems 
to be some incomplete code in neighbour but at least EMBOSS should gracefully 
load them. That will take a little more effort because it involves some changes 
to our port of neighbour, but is not difficult (he says confidently!)

We also need to update the phylip code in EMBOSS to the latest release.

It would help to know how many users are working with the EMBOSS phylip.

regards,

Peter Rice