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mac default iconcoalescent For Mac Publisher's description

In continous time coalescent the waiting event is moving from k to k-1 ancestral lineages.

Points to Ponder

1. In continous time coalescent the waiting event is moving from k to k-1 ancestral lineages. But the discrete time coalescent was defined using a different waiting time event namely, moving from k to less than k lineages. But how the definition of the waiting time changed was not clear.
2. As I understood, the effect of approximation in Hein`s book (page 23) should be -2/100 rather than -3/100. This is because we are approximating the prob. of the waiting time event and the waiting time event is to have less than k lineages from k lineages.
3. Ewen`s distribution as a sampling distribution from the equilibrium distribution of the poisson process of mutations. (John talked about this in the first presentation)
4. Boundary condition of the K alleles recursion: p(e_j)=ПЂ_j where ПЂ_j is the equ. dist., whereas boundary condition for KC64 is p( {1} ) = 1 which is true for any sample.

Topics Pending

1. Population simulation of the Wright-Fisher model.
2. Refreshers on geometric and exponential distribution. Relevant results.
3. Discrete time coalescent using geometric distribution. Coalescent of 2 genes. Coalescent of k genes (waiting time event is defined as to have less than k ancestral lineages) and its approximation. Effect of approximation. Continuous time coalescent (waiting event is changed as to have k-1 ancestral lineages) and its algorithm to simulate a sample gnealogy. The height of the tree and the total branch length of the tree.

Topics Included

1. Wright-Fisher reproduction model
2. Recursions for infinite alleles model (KC64) and infinite sites model(K69). Also GT94 recursion for K69.
3. Discussion on the benefits of straightforward implementation of KC64 and K69 and their limitations, providing motivation for more efficient exact solutions and widely applicable approximate methods based on importance sapling.

What's New in This Release:

В· streamlined the input architecture much.
В· Check phylogeny using Gusfield`s Algorithm ID:512797923
В· Compute genealogies in Recursion ID:1256846304
В· countGenealogies(): this is always computed. For exact, this counts all geanlogies used in both exact and sampling based methods. In the eaxct, all are distinct but in the latter duplicates are possible.
Compute genealogies in Recursion ID:
В· rememberGenealogies(boolean), when enabled, remembers the genealogies computed in next computation.
В· genealogies(): List, when enabled returns the genealogies used, else an empty list. In exact implementation this keeps all the genealogies and in sampling based approximate methods this returns the distinct genealogies sampled.
В· nclude GT94 data in files. ID: 2089265130

System Requirements:

В· Java
Program Release Status: Minor Update
Program Install Support: Install and Uninstall

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