Question: Distance Tree For Gerp
2
gravatar for Darked89
7.9 years ago by
Darked894.2k
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.

EDIT

Got one dictance tree here: http://genomewiki.ucsc.edu/index.php/Phylogenetic_Tree

conservation phylogeny • 1.7k views
ADD COMMENTlink modified 7.9 years ago by Arelicorlaior50 • written 7.9 years ago by Darked894.2k
2
gravatar for Javier Herrero
7.7 years ago by
Javier Herrero290 wrote:

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

ADD COMMENTlink written 7.7 years ago by Javier Herrero290
1
gravatar for Arelicorlaior
7.7 years ago by
Arelicorlaior50 wrote:

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

http://www.timetree.org/index.php?taxon_a=Homo+sapiens&taxon_b=Macaca+mulatta

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 11 weeks ago by RamRS25k • written 7.7 years ago by Arelicorlaior50
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