Re: Lineage selection

> Computing the distance between parents and pruning them as needed is more
> space efficent (no additional space needed) and likely to be just as quick
> , as to keep a history of a genomes ancestral tree one is going to have to
> use a lot of space to do it fast (giving each new genome a number and
> keeping track of that sorted with the distance from the current child) or
> compute it slowly using a more minimal encoding (keeping a refence to
> parents and searching through that).

One thing I could remind for that performance talk that individuals can be
very complex. It should be remembered when we start to calculate those
diferences using structures. My lineage method is simple. for example
keeping 100 parents integers in sorted having
info what generation those existed it is nothing in complex individuals, or
when evaluation is slow. So it partically very fast, I just want it faster
and sorted array sounds simple and good. Instead structure difference
computing using greps, huh, I don't like idea at all.

> I really don't think keeping track of lineages is more biolically
> plausible than any of the other methods and as the number of genomes grows
> larger it gets more biologically implausible.
Kind of agree, if you could also say what you see biologically realistic and
fast method.

t. Harri
"Nicholas King" <ze@xxxxxx> kirjoitti
viestissä:4371749f$0$14254$5a62ac22@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> Kent Paul Dolan wrote:
>> "hmm" <harri.salakoski@xxxxxxxxxxx> wrote
>>
>>
>>>fast?
>>
>>
>> Agreeing with both you and Lionel B, I'd like to offer the
>> idea to (perhaps temporarily for the mating) encode your
>> genomes in some limited size alphabet, then use the agrep
>> (approximate general regular espression parser) program to
>> match individuals who are "close" (within some set number
>> of differences) but exclude those who are "too close" (your
>> own algorithm) to find mates.
>>
>> The reason for this recommendation is that agrep can be very
>> fast, what you were seeking.
>>
>> Google for the agrep web site.
>>
>> HTH
>>
>> xanthian.
>>
>>
>>
>>
> I really don't think that agrep can be much faster than a simple
> computation of distance since computing the distance between 2 strings is
> 0(N).
>
> Computing the distance between parents and pruning them as needed is more
> space efficent (no additional space needed) and likely to be just as quick
> , as to keep a history of a genomes ancestral tree one is going to have to
> use a lot of space to do it fast (giving each new genome a number and
> keeping track of that sorted with the distance from the current child) or
> compute it slowly using a more minimal encoding (keeping a refence to
> parents and searching through that).
>
> If i was going to do linage selection as proposed by hmm i'd keep track of
> the 'n' most recent parents in a sorted array and their age.
>
> The problem being the further one wants to go back the larger the search
> space. The search space grows at a a rate of 2^depth.
>
> I really think that if one is looking at speciation then a distance metric
> between genomes or using one of the geographical models is the best
> choice.
>
> I really don't think keeping track of lineages is more biolically
> plausible than any of the other methods and as the number of genomes grows
> larger it gets more biologically implausible.
>
> The most that happens with linage is that if one ancestors are too close
> then there is a social taboo against inbreeding.


.

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