Setup wiki documentation for the current milestone:
Basics about libpll. Partition structure, how to setup a partition.
Explain how tip vectors should look like in a typical phylogenetic analysis (given a solid and a degenerate character)
The two ways of setting tip vectors (set clv manually or pass sequence and map)
How to parse FASTA files (complete or partial parse)
How to parse newick files (rooted and unrooted)
How to setup frequencies, rate heterogeneity, substitution parameters
Explain what is a rate matrix (R), an instantaneous rate matrix (Q-matrix) and a transition probability matrix (P-matrix). Show all the gory details of creating a p-matrix (normalization at diagonal etc). Give a description of the GTR.
How to compute the p-matrices with the library (update_prob_matrices) given the branch lengths
How to compute the CLV vectors (pll_update_partials)
How to evaluate the log likelihood of a rooted tree (pll_compute_root_loglikelihood)
How to evaluate the log likelihood of an unrooted tree (pll_compute_edge_loglikelihood)
Setup wiki documentation for the current milestone:
Basics about libpll. Partition structure, how to setup a partition.Explain how tip vectors should look like in a typical phylogenetic analysis (given a solid and a degenerate character)The two ways of setting tip vectors (set clv manually or pass sequence and map)How to compute the CLV vectors (pll_update_partials)Document all protein models, give referencesDocument the demo examples