Question: Branch length and maximum likelihood
0
6 months ago by
dflkjfdljfs0 wrote:

For phylogenetics, say you have a tree and calculate the maximum likelihood of two sites. If site 1 is less likely than site 2, how would you alter the branch lengths to make site 1 more likely? Would you increase or decrease the branch lengths?

Or, you can answer this question: if you have a higher branch length, is the maximum likelihood going to be bigger?

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modified 6 months ago by Mensur Dlakic6.6k • written 6 months ago by dflkjfdljfs0

What do you mean by "site" and "less likely"?

ADD REPLYlink written 6 months ago by Asaf8.4k

I mean two sites of two different sequences. By less likely, I mean a smaller posterior probability

ADD REPLYlink written 6 months ago by dflkjfdljfs0

Sorry I'm just learning bioinformatics.

ADD REPLYlink written 6 months ago by dflkjfdljfs0

Sorry, I still didn't understand your question, consider revising it or adding a figure

ADD REPLYlink written 6 months ago by Asaf8.4k

Okay so how about would a larger branch length make the maximum likelihood bigger?

ADD REPLYlink written 6 months ago by dflkjfdljfs0
0
6 months ago by
Mensur Dlakic6.6k
USA
Mensur Dlakic6.6k wrote:

Branch length (BL) and posterior probabilities (PPs) are not correlated variables between themselves, or even with regard to maximum likelihood (ML). You can think of the first two as "local" variables that describe distances between tree members (BLs) or how likely a particular branch topology is (PPs). Following that analogy, ML is a "global" variable that describes the relative fitness of the whole tree topology.

What this means is that we can have identical BLs but different PPs of the same branch in two different contexts. It also means that if you add a new member to a tree, the ML with change (it will decrease) even if the overall topology, individual BLs and PPs remain the same. In a nutshell, ML is negatively correlated with the alignments size (# columns * # members). BLs are positively correlated with member distances. PP estimates how likely a given topology is, which in general is not correlated with either BLs or ML.

ADD COMMENTlink written 6 months ago by Mensur Dlakic6.6k
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