My name is Rui Borges and I am developing a research study on fish lineage specific duplications in CIIMAR, Portugal. For the study I am using Diverge v2.0 to find which amino acids are responsible for the functional diverge between those duplications. In the first version of Diverge it is explained how to calculate theta I statistical significance, however for theta II it is not explained. So, I am asking you how to assess the significance of the theta II parameter, since the LRT value is not given. Sorry if it is a very simple question. I read so many papers that use diverge and they just refer a z-score and then the related p-value that I don't know where they are in the output. I hope you may help me in this issue and thank you in advance for any time wasted on this issue. Rui
In reading hundreds of questions on this forum, I have not see mention of the tool Diverge v2.0. Thus, an example of input/output or expected result may be needed in order to get some help.
This an example output:
Da 0.58711 Db 0.90099 N 280 C 34 R 25 Alpha ML 0.52999 Theta-II -0.04351 Theta SE 0.05786 Ar -0.06641 PIr 0.31213 p 0.17404 d 0.19121 W 0.46926 Z 0.49232 Gr 0.42373 Gc 0.57627 h 0.08655 Q 0.96154 F00,N 0.48968 F00,R 0.00590 F00,C 0.00295
N, C, and R are the numbers of sites across internal nodes (a, b) of the tree that display no difference, conserved difference, and radical differences, respectively, and p is the proportion of (overall) differences between nodes a and b. Da and Db are the average numbers of substitutions per sites in clusters A and B, re
GeneA/B Da 0.58711 Db 0.90099 N 280 C 34 R 25 Alpha ML 0.52999 Theta-II -0.04351 Theta SE 0.05786 Ar -0.06641 PIr 0.31213 p 0.17404 d 0.19121 W 0.46926 Z 0.49232 Gr 0.42373 Gc 0.57627 h 0.08655 Q 0.96154 F00,N 0.48968 F00,R 0.00590 F00,C 0.00295
N, C, and R are the numbers of sites across internal nodes (a, b) of the tree that display no difference, conserved difference, and radical differences, respectively, and p is the proportion of (overall) differences between nodes a and b. Da and Db are the average numbers of substitutions per sites in clusters A and B, respectively, and d is the dist