Questions tagged [positive-selection]

Technical description in evoluionary biology where a mutation results in a fitness advantage

Filter by
Sorted by
Tagged with
-1 votes
1 answer
32 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. ...
user avatar
  • 107
0 votes
0 answers
37 views

Selection analysis based on each leaves as foreground with FastCodeML

I have to test the selection for each leaves in a phylogenetic tree. In normal case(with codeml), I will be running model zero for all leaves and then model 2 for each leaves as foreground (marking ...
user avatar
  • 1
1 vote
1 answer
29 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 ...
user avatar
1 vote
1 answer
33 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 ...
user avatar
1 vote
1 answer
35 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 ...
user avatar
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 ...
user avatar
  • 127
0 votes
1 answer
371 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). ...
user avatar
3 votes
1 answer
208 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 ...
user avatar
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 ...
user avatar
  • 203
7 votes
1 answer
876 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 ...
user avatar