Initial trees

[Thomas Fisher-York]

Do all the individuals in the population start from the same tree? Or if they are random does each individual get an independent random tree? How about if reading the initial tree from a file or using stepwise? Is it possible to make garli read in a distinct tree for each individual? Thanks.

[Derrick Zwickl]

Hello,

Yes, all individuals start from the same tree, whether a random, stepwise addition or user tree.  Population sizes are very small (4 individuals by default) and selection pressure is strong, so having multiple different trees would result in only one tree leaving offspring into the next generation anyway, unless the likelihoods of the trees were extremely similar.  In other words, if the initial population were started from different tree the population state at the second generation would be just like it is at the first generation when all individuals start from the same tree.  Allowing multiple trees might not be a bad idea, since it would at least start the search from the best of several options, but that isn't currently implemented.

Best,
Derrick

On 12/4/14 12:30 PM, Thomas Fisher-York wrote:

Do all the individuals in the population start from the same tree? Or if they are random does each individual get an independent random tree? How about if reading the initial tree from a file or using stepwise? Is it possible to make garli read in a distinct tree for each individual? Thanks.

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