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DATE 2016-10-01

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MESSAGE
DATE 2016-10-27
FROM Ruben Safir
SUBJECT Re: [Learn] Phylogenetics educational links
From learn-bounces-at-nylxs.com Thu Oct 27 22:47:54 2016
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References: <8a528f28-6298-2fe8-0a01-8899000d0244-at-mrbrklyn.com>
<8760odd05h.fsf-at-contrapunctus.net>
From: Ruben Safir
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Date: Thu, 27 Oct 2016 22:47:49 -0400
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Subject: Re: [Learn] Phylogenetics educational links
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On 10/27/2016 04:09 PM, Christopher League wrote:
> =

> Here's a set of introductory slides on inference of phylogenetic trees.
> =

>
> =

> Based on what I've learned today, "small" parsimony algorithms like
> Fitch and Sankoff rely on labeling a *given* tree shape (aka topology),
> so we already have to know (or hypothesize) the ancestral relationships.
> The algorithm just determines which labels (mutations) to assign to
> interior nodes. That's really unsatisfying to me.
> =

> But the "big" parsimony techniques have to search the entire tree space,
> which is ENORMOUS. The problem is formally NP-hard. Now -- people do
> manage to solve (or approximately solve) NP-hard problems every day by
> using piles of dirty tricks. When it comes to searching gigantic spaces,
> those dirty tricks are the classic techniques of artificial
> intelligence.
> =

> So the lecture slides get into techniques like greedy algorithms,
> hill-climbing, simulated annealing, genetic algorithms, etc. Anyway,
> there could be a lot of meat here that fits under the heading of AI +
> phylogenetics. It's much more accessible stuff than trying to
> automatically interpret 3D model data to take measurements of maxillary
> bones.
> =

> CL
> =

> =

> Ruben Safir writes:
> =

>> http://telliott99.blogspot.com/2010/03/fitch-and-sankoff-algorithms-for.=
html
>>
>> "The Fitch algorithm considers the sites (or characters) one at a time. =
At each tip in the tree, we create a set containing those nucleotides (stat=
es) that are observed or are compatible with the observation. Thus, if we s=
ee an A, we create the set {A}. If we see an ambiguity such as R, we create=
the set {AG}. Now we move down the tree [away from the tips]. In algorithm=
ic terms, we do a postorder tree traversal. At each interior node we create=
a set that is the intersection of sets at the two descendant nodes. Howeve=
r, if that set is empty, we instead create the set that is the union of the=
two sets at the descendant nodes. Every time we create such a union, we al=
so count one change of state."
>>
>>
>> https://en.wikipedia.org/wiki/Non-parametric
>> Nonparametric statistics are statistics not based on parameterized famil=
ies of probability distributions. They include both descriptive and inferen=
tial statistics. The typical parameters are the mean, variance, etc. Unlike=
parametric statistics, nonparametric statistics make no assumptions about =
the probability distributions of the variables being assessed. The differen=
ce between parametric models and non-parametric models is that the former h=
as a fixed number of parameters, while the latter grows the number of param=
eters with the amount of training data.[1] Note that the non-parametric mod=
el does, counterintuitively, contain parameters: the distinction is that pa=
rameters are determined by the training data in the case of non-parametric =
statistics, not the model.
>>
>> https://en.wikipedia.org/wiki/Fitch-Margoliash_algorithm
>> Distance-matrix methods
>>
>> Distance-matrix methods of phylogenetic analysis explicitly rely on a me=
asure of "genetic distance" between the sequences being classified, and the=
refore they require an MSA (multiple sequence alignment) as an input. Dista=
nce is often defined as the fraction of mismatches at aligned positions, wi=
th gaps either ignored or counted as mismatches.[1] Distance methods attemp=
t to construct an all-to-all matrix from the sequence query set describing =
the distance between each sequence pair. From this is constructed a phyloge=
netic tree that places closely related sequences under the same interior no=
de and whose branch lengths closely reproduce the observed distances betwee=
n sequences. Distance-matrix methods may produce either rooted or unrooted =
trees, depending on the algorithm used to calculate them. They are frequent=
ly used as the basis for progressive and iterative types of multiple sequen=
ce alignment. The main disadvantage of distance-matrix methods is their ina=
bility to efficiently use =

>> information about local high-variation regions that appear across multi=
ple subtrees.[2]
>>
>>
>> -- =

>> So many immigrant groups have swept through our town
>> that Brooklyn, like Atlantis, reaches mythological
>> proportions in the mind of the world - RI Safir 1998
>> http://www.mrbrklyn.com =

>>
>> DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
>> http://www.nylxs.com - Leadership Development in Free Software
>> http://www2.mrbrklyn.com/resources - Unpublished Archive
>> http://www.coinhangout.com - coins!
>> http://www.brooklyn-living.com
>>
>> Being so tracked is for FARM ANIMALS and and extermination camps,
>> but incompatible with living as a free human being. -RI Safir 2013
>> _______________________________________________
>> Learn mailing list
>> Learn-at-nylxs.com
>> http://lists.mrbrklyn.com/mailman/listinfo/learn
> =

> =

> =

> _______________________________________________
> Learn mailing list
> Learn-at-nylxs.com
> http://lists.mrbrklyn.com/mailman/listinfo/learn
> =


Since there are n OTUs to insert, the outer loop iterates n
=E2=88=92
1 times.
When there are n leaves in the tree, there are
2n
=E2=88=92
1 places to insert the new OTU, and determining the cost of the result
requires O(n)time. Thus, a greedy algorithm for inferring a phylogeny is
O(n3).


Any chance you can explain this better? How did it get the N cubed?
I'm sick of not understanding this.


-- =

So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
proportions in the mind of the world - RI Safir 1998
http://www.mrbrklyn.com

DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
http://www.nylxs.com - Leadership Development in Free Software
http://www2.mrbrklyn.com/resources - Unpublished Archive
http://www.coinhangout.com - coins!
http://www.brooklyn-living.com

Being so tracked is for FARM ANIMALS and and extermination camps,
but incompatible with living as a free human being. -RI Safir 2013
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Learn mailing list
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  1. 2016-10-04 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Check List of Texts to learn Cladistics and
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  3. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Library access
  4. 2016-10-04 Christopher League <christopher.league-at-liu.edu> Re: [Learn] phylogenetics
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