Distance Tree For Gerp

Question

[Darked89]

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

Answer 1

[Javier Herrero]

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

Answer 2

[Arelicorlaior]

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.

Answer 3

[514269236]

Hey, I met many difficults in using gerp/gerp++, but succeed to solve them. I'm very excited and want to share your the solution.

You can find the solution and some examples (input, output) in here https://github.com/XDcat/GerpHelper.

[Diana]

Hey, thanks for that. When in Github you say:

Update 2022.10.28

I found the code from github can't run.

were you by any chance getting this error:

Segmentation fault

?