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Background & References


Siepel Lab

Major Programs

phastCons: Conservation scoring and identification of conserved elements

phastOdds: Log-odds scoring for phylogenetic models or phylo-HMMs

phyloFit: Fitting of phylogenetic models to aligned DNA sequences

phyloP: Computation of p-values for conservation or acceleration, either lineage-specific or across all branches

exoniphy: Phylogenetic exon prediction

dless: Prediction of elements under lineage-specific selection

prequel: Probabilistic reconstruction of ancestral sequences

phastBias:Identification of GC-biased gene conversion using a phylo-HMM


Alignments: maf_parse, msa_view, msa_split, msa_diff

Phylogenetic models: tree_doctor, all_dists, draw_tree, consEntropy, indelFit, indelHistory

Sampling/bootstrapping: base_evolve, phyloBoot

Annotations: refeature, clean_genes, eval_predictions

...and others


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