Questions tagged [positive-selection]
Technical description in evoluionary biology where a mutation results in a fitness advantage
10
questions
-1
votes
1
answer
33
views
Evolutionary speaking, what are the constraints on having new mutations?
Evolutionary speaking, some mutations lead to better fitness of an organism and its adaptation to the environment changes, but I was wondering if there are some constraints on having new mutations. ...
- 107
1
vote
1
answer
55
views
Selection analysis based on each leaves as foreground with FastCodeML
I am using positive selection analysis for each leaves in a phylogenetic tree.
In the routine calculation via codeml, I will be running model zero for all leaves ...
- 11
1
vote
1
answer
36
views
Measure the purifying selection for certain taxa along a phylogeny
I am posting this message because I need clarity about the analysis I want to perform.
In my analysis, I have a homologous gene in 13 species, and I would like to evaluate the selection pressure of ...
- 199
1
vote
1
answer
42
views
panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis
I am using godon to find genes under positive selection with the branch-site test. However, after running for a little while I get the error "panic: division ...
1
vote
1
answer
36
views
What are the p01sum and p0prop parameters in godon?
When using branch-site model in Godon, model optimization results include the following parameters: p01sum and p0prop. What are ...
- 2,705
1
vote
0
answers
24
views
Gene size and power of detection in sequence divergence analyses
I want to look at violation of the strict molecular clock and compare dn/ds ratio to test differences in evolutionary rates in a set of genes. Some of these genes are really short (30AA), is it likely ...
- 127
0
votes
1
answer
443
views
PAML branch-site model: Identical lnL value between null and alternative models?
I have been running PAML, via codeml, to try to identify positive selection in certain branches of my tree for one gene (but will eventually be trying to automate the analysis over multiple genes). ...
- 79
3
votes
1
answer
285
views
Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?
I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
- 79
4
votes
2
answers
2k
views
How can I use Arlequin via the command line?
I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin ...
- 203
7
votes
1
answer
939
views
How to run HYPHY on multiple files non-interactively?
I would like to test for positive selection in a large set of genes.
I want to have a yes/no answer to the question if gene was evolving under positive selection. Therefore I chose model BUSTED for ...
- 2,705