Dear Colleagues , I prepare a BAM/SAM file from mapping the raw RNA seq reads against a Trinity-build de novo reference transcriptome . I am wondering if there is any simple pipeline/packages to estimate basic statistics such as : per site synonymous/ non- synonymous diversity, heterozygous deficiency(Fis) , number of synonymous/non synonymous segregating sites and etc . I use to use bio++ . I guess there are other ways too. Thanks in advance