Variety of Formulae

1. Nucleotide Diversity

Screenshot from 2016-12-30 20-44-52

where xi and xj are the respective frequencies of the ith and jth sequences, πij is the number of nucleotide differences per nucleotide site between the ith and jth sequences, and n is the number of sequences in the sample.

2. variance

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3. the average k-mer coverage

如果k=L, 根据公式,那么Ckmer=0。但是这明显是错的,实际应该是1,因为,每个k-mer(reads),至少被覆盖了一次。而在k=L的极端情况下,只会存在少量频率大于1的k-mer。因为reads之间,除了PCR duplication会生成完全相同的reads,一般情况下,两条reads完全相同的概率是非常小的。

4.

Timeline of genus Bos

bos_species

source:http://www.timetree.org/

TimeTree is a public knowledge-base for information on the tree-of-life and its evolutionary timescale. For those interested in published summaries of relationships and divergence times of major groups of organisms, see publications from Hedges and Kumar (2009) and Hedges et al. (2015). For reviews of the history and methods of time estimation, and other useful information, see RESOURCES. TimeTree is jointly directed by Blair Hedges and Sudhir Kumar (Temple University). We encourage suggestions for improvement of this resource (see CONTACT). Current staff members include: Glen Stecher, Bremen Braun, and Michael Suleski (Software and Database Developers), and Julie Marin, and Sarah Hanson (Data Research and Assembly). Previously we have been assisted by Brooke Gattens, Michael McCutchan, Kelly Boccia, Wayne Parkhurst, Tina Dennison, Mandy Hippenstiel, Audrie Kapinus, Lainey Lee, Jaclyn McKay, Molly Oberholtzer, Davide Pisani, Kathy Plavnik, Prachi Shaw, Lidsay Stork, Vinod Swarna, Graziela Valente, Curtis Williams, and Lin-Wei Wu. We continue to receive helpful feedback from our colleagues in the evolutionary biology community. This project has been supported, in part, by grants from the National Science Foundation, NASA Astrobiology Institute, and Science Foundation of Arizona.