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f^2(ab) = 4f(aa)f(bb)
Wright-Fisher
-species is monecious
-generations are non-overlapping
-each generation is produced from prev by random mating
-no selection, mutation, or migration
pij = P(X(t+1) = j|X(t)=i) = (2N choose j) * (i/2N)^j * (1-(i/2N))^(2N-j)
difference equations
f(t+2) = a*f(t+1) + b*f(t)
r^2 = a*r + b
x(t) = A*a^t + z(t) // for some constant A
Selection
AA>Aa>aa:lim of fA(t) = 1
heterozygous: p = (WAa-Waa)/(2*WAa WAA Waa) lim of fA(t) = p
homozygous: calc p and then see if fA(0) (</=/>) p and that's the answer
cobwebbing
stable point is intersection between y = phi(x) and y=x and when points around it circle towards it, not
away
also, if |phi'(x)| < 1 then point x is stable
you can actually circle around a point without spiraling inwards or outwards
markov chain
P(X(n) = j | X(n-m) = i) = the sum over all the possible paths from time n-m to time n to get from state i
to state j
prow/col = prob of going from row value to col value
p(0) = [P(X(0)) = 0 ... P(X(0) = n)]
P(X(t) = j) = p(0) * A^t // mult p(0) down approp column (jth column) of A^t
E[X(t)] = p(0) * A^t * g // mult g values across row of A^t for each value/index in p(0)
"show E[h(X(t+1))|X(t) = i)] = h(i)" - show A*h = h
irreducible = every state communicates with each other
stationary distro: sum(pi's) = 1 and pi's = pi's * A // pi0 = pi0 * A00 + ... + pin * An0
"if chain in state i at t, how long until until state i again?" - 1/pii
shotgun sequencing
Xi denotes leftmost point of frag i
expected coverage: E[C] = 1 - e^(-N * E[L] / g)
prob frag is isolated: (1-(2L/g))^(N-1) = e^(-2NL/g)
below vvv -- a denotes position of X1
reasoning: frag j does not overlap frag 1 iff Xj not in interval [a-L, a+L] which is (1-2L/g). for this to
occur for each other frag, then you get equation
expected # of isolated frags: Ii = 1 if i is isolated -> sum from 1 to N of E[Ii] = N * e^(-2NL/g)