search

PoonLab / vindels

Developing an empirical model of sequence insertion and deletion in virus genomes
1 stars 0 forks source link

Fit slippage model to insertions data set #87

Closed ArtPoon closed 4 years ago

ArtPoon commented 4 years ago

This may be closely related to the Thorne-Kishino-Felsenstein (TKF91) model: https://link.springer.com/article/10.1007/BF02193625

TKF91 only allows indels of length 1 (geometric model). Subsequent work have relaxed this assumption to allow for longer indels.

jpalmer37 commented 4 years ago

I've mainly been following the Felsenstein book and have found it quite helpful. In addition to that, this is a link I've been looking at.

jpalmer37 commented 4 years ago

These are the results of an affine gap model with parameters p.enter and p.stay that describe the probability of entering and staying within a slip state, respectively.

affine-posterior affine-trace

I'll continue trying more complicated models (e.g. changing slip positions and having a penalty value applied to all indels that are not a multiple of 3).

jpalmer37 commented 4 years ago

A website I was looking at: http://pages.stat.wisc.edu/~larget/Genetics629/outline5.pdf

EDIT: Misleading and probably shouldn't be looked into further.