[EMBOSS] Segmentation fault with multiple similarity matricies in fneighbor

[Peter Rice]

Dear Hazel,

> fneighbour  (and ffitch and fkitsch - they also have this bug) should 
> definitely support multiple input matrices, as the original Phylip routines
> do. It is a very desirable trait because it is needed to create bootstrap
> values for trees built from distance matrix data.

I have a fix ... but would like more input data to test. Can you send me an
example input file to run through both EMBASSY fneighbor and the original
neighbor. (Better still, an example set of pseudo sequences to run through the 
remainder of your script)

> The desired behaviour is for fneighbor (and ffitch and fkitsch) to accept 
> input files containing multiple distance matrices and produce multiple trees
> from them, in standard nested-parenthesis notation, which can then be read by
> fconsense.
> 
> The reading should not stop at the end of the first distance matrix, or the 
> fault will become silent, and the user familiar with Phylip may not notice 
> that the extra matrices have been dropped until many processing steps later.

Yes indeed. The fix reads all distance inputs as multiple sets (we already read
tree data as multiple trees) and processes each in turn.

regards,

Peter Rice