Lab Notebook: June 28

Met with Ryan today to discuss the rate-partitioning project.

* Generate trees. Star phylogeny, whatever works.
* Use simSeq() in phangorn or seqgen in phyclust to simulate sequence data. This should be the GTR+gamma with 4 rate categories, just to start with.
* Use HyPhy to estimate rates. This will require me to either fix the current version of HyPhy to compile a single-threaded version, or use the old version of HyPhy compiled for tapir.
* Use rate-partitioning to partition the sequences based on rate and then try to infer a tree based on that.

Some things to think about:

* Is there a sequence generation algorithm which will create indels? Missing data in our alignments are the reason we are using HyPhy to estimate rates.