Question: Distance Tree For Gerp
gravatar for Darked89
8.5 years ago by
Barcelona, Spain
Darked894.2k wrote:

I would like to calculate GERP scores for few genomic regions from non-model organism A (mammal). Lets assume I will get genomes from 10 other species, be it closely related to A, good quality genomic sequence, etc.

Few questions:

  1. can I get some precalculated distance trees from some database?
  2. if not, what is the proper method to calculate distance tree for my set of species?
  3. assuming I got a tree with 20 species in it, but want to create genomic alignments for just 10+1 species, can I still use this tree or GERP will crash?

I will be also very thankful for any working GERP HowTos.


Got one dictance tree here:

conservation phylogeny • 1.8k views
ADD COMMENTlink modified 8.5 years ago by Arelicorlaior50 • written 8.5 years ago by Darked894.2k
gravatar for Javier Herrero
8.4 years ago by
Javier Herrero300 wrote:

Answering your 3rd point, GERP will ignore the species from the tree that are not in the alignment.

ADD COMMENTlink written 8.4 years ago by Javier Herrero300
gravatar for Arelicorlaior
8.4 years ago by
Arelicorlaior50 wrote:

You can use to estimate divergence distances between two species. Although not complete, it's one of the best resources out there:

Apart from timetree, the NCBI taxonomy database also contains a phylogeny for most known species, but it doesn't have distance estimates, just a topology. Combining one and the other, you can get a tree of distances for your list of species.

ADD COMMENTlink modified 10 months ago by RamRS28k • written 8.4 years ago by Arelicorlaior50
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