| baseml wrapper This program utilizes the baseml package of PAML to generate nucleotide substitution rates of sequence alignments. It incorporates both single and double bootstrap to allow creation of sequence replicas and generation of a mean, median, and confidence intervals for each branch in the target pyhlogeny. It has been incorporated into the galaxy framework, and it is open-source. http://www.bx.psu.edu/cgi-bin/trac.cgi/ |
| AlphaSubst / M-DEA AlphaSubst incorporates the baseml module of PAML, single and double bootstrap algorithims, and substitution model variance to determine the magnitude of male mutation bias between two different types of chromosomes. Analysis can either be performed on a single loci or across a group of alignments. It has been integrated into the galaxy framework, and is open source. http://www.bx.psu.edu/cgi-bin/trac.cgi/ |
| X inactivation http://www.bx.psu.edu/makova_lab/Doc/X_Inactivation.htm |
| rhemac_alpha This is the collection of scripts, libraries and data used to find the alpha (male-mutation bias) in the rheMac2 genome build. A README will be available Feb. 1, 2007. http://www.bx.psu.edu/makova_lab/software/rheMac_alpha/ |