RemoveDashes.py
This python script cleans Fasta alignmnents prior to performing tests for positive selection: it deletes "columns" that contain at least one gap or any non-base symbols (i.e. not A, C, G, or T).
nonCodingSelection.bf
This is a HyPhy batch file (http://hyphy.org/w/index.php/Main_Page)
for testing for signatures of positive selection in non-coding sequences. T
he method is an improved version of EvoNC (W.S.W. Wong and R. Nielsen. (2004)
Detecting Selection in Noncoding Regions of Nucleotide Sequences. Genetics, Vol. 167, 949-958)
into a modified branch-site model (J. Zhang, Z. Yang, and R. Nielsen.
(2005) Evaluation of an Improved Branch-Site Likelihood Method for
Detecting Positive Selection at the Molecular Level. Mol Biol Evol 22
(12): 2472-2479).
This script allows to use introns or synonymous substitutions from nearby coding sequences as neutral proxies for testing . You can choose to look at positive selection on any branch and run a Naive Empirical Bayes or Bayes Empirical Bayes algorithm (Z. Yang, W.S.W. Wong, and R. Nielsen. (2005) Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection. Mol Biol Evol (2005) 22 (4): 1107-1118) to detect what sites are under positive selection, negative selection, or neutral.
Various versions of this script have been used in the following manuscripts:
- Fedrigo O., A.D. Pfefferle, C.C. Babbitt, R. Haygood, C.E. Wall, and G.A. Wray. (2011) Multiple lines of evidence link glucose transporters to human brain evolution. Brain, Behavior and Evolution. 78:315–326.
- Pfefferle A.D., L.R. Warner, C.W. Wang, W. J. Nielsen, C.C. Babbitt, O. Fedrigo, and G.A. Wray. (2011) Comparative expression analysis of the phosphocreatine circuit in extant primates: Implications for human brain evolution. Journal of Human Evolution. 60(2):205-12.
- Cruz-Gordillo P., O. Fedrigo, G.A. Wray, and C.C. Babbitt. (2010) Extensive Changes in the Expression of the Opioid Genes between Humans and Chimpanzees. Brain, Behavior and Evolution.76:154-162.
- Haygood R., O. Fedrigo, and G.A. Wray. (2008) Reply to "Rapidly evolving human promoter regions. Nature Genetics. 40(11): 1263-1264.
- Haygood R., O. Fedrigo,B. Hanson, K.-D. Yokoyama, and G. A. Wray.(2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nature Genetics. 39(9): 1140:1144.