[Bioperl-l] Bio::Species, Bio::Taxonomy::Node overhaul

[Sendu Bala]

Hilmar Lapp wrote:
> On Aug 7, 2006, at 9:57 AM, Sendu Bala wrote:
> 
>> Let T be a rooted tree. A node x ∈ T is an ancestor of a
>> node y ∈ T if the path from the root of T to y goes through
>> x. A node v ∈ T is a common ancestor of x and y if it is
>> an ancestor of both x and y. The nearest common ancestor,
>> nca, of two nodes x, y is the common ancestor of x and y
>> whose distance to x (and to y) is smaller than the distance
>> to x of any other common ancestor of x and y.
>>
>> According to that, v cannot be x or y.
> 
> Why not? The path from the root node to node x certainly goes through  
> x, so x is an ancestor of x.

Well, 'through' implied to me 'does not end at'. Maybe it's not supposed 
to imply that, in which case what you say seems fair.

In any case, since its debatable I'll go with the old expected 
behaviour. I'll still leave the changes in PAML et al. that use the 
single call to get_lca, as that will be faster.

The other point of contention was with what Bio::Species::species should 
return, and again since its debatable I'll go with the old expected 
behaviour (guess badly what the specific name is).

I'll wait till this weekend for any more comments and then commit and 
add to the wiki.