codemlz README Author: Zhengting Zou (ztzou@umich.edu) Version 0.1 (2016-05-17) Description: This is a modified version of codeml included in the PAML4.8 package (Author: Ziheng Yang). This modifed version can calculate a new parameter, eta, which is the relative selection coefficient of non-synonymous transitions if considering that of non-synonymous transversions is 1. The following parameters need to be fixed in the codeml.ctl file (i.e. other models and choices not implemented): ################ seqtype = 1 clock = 0 model = 0 NSsites = 0 Mgene = 0 fix_alpha = 1 alpha = 0. ################ Tests have been rather limited and more to follow. ABSOLUTELY NO WARRANTY. All copyright reserved. Please contact the author before usage of any purposes. I'm open to proper collaboration proposal. Thanks.