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brettc / partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.
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add a branchlengths=equal option #40

Closed roblanf closed 8 years ago

roblanf commented 9 years ago

RAxML has only two models for branch lengths currently:

  1. All branch lengths equal
  2. Each partition has its own set of branch lengths.

The latter corresponds to 'unlinked' branch lengths in PF (i think it's by using the option -M)

The former is not implemented in PF, but could be as an 'equal' branch lengths option.

Note that right now, RAxML doesn't implement anything that's equivalent to what we call 'linked' branch lengths, where there's an underlying set of branch lengths but each partition gets its own rate multiplier. This is a shame, because it's my suspicion that this is by far the best of the three approaches (i.e. out of 'unlinked', 'linked', and 'equal').

roblanf commented 8 years ago

small update.

RAxML does implement linked branch lengths with '-f B', but not in combination with searching for a tree. This option was built for us, and will only optimise a set of branch lengths scalars given an input tree WITH BRANCH LENGTHS. I.e. it will not optimise the underlying set of branch lengths, only the scalars.

roblanf commented 8 years ago

On reflection, I think this is pointless. It adds complexity, and this is going to be a model that will almost never be useful.