Table 1:

Selected programs in PHAST

Program	Description	RPHASTa	References
dless	Prediction of elements under lineage-specific selection		[28]
exoniphy	Phylogenetic exon prediction		[29]
phastCons	Conservation scoring and identification of conserved elements	✓	[3]
phyloFit	Fitting of phylogenetic models to aligned DNA sequences	✓	[20]
phyloP	Computation of P-values for conservation or acceleration, either lineage specific or across all branches	✓	[23]
prequel	Probabilistic reconstruction of ancestral sequences		–
base_evolve	Simulation of synthetic alignments from phylogenetic models	✓	–
clean_genes	Filtering of gene annotations based on conservation properties		–
indelHistory	Inference of phylogenetic indel histories for alignments, based on a simple algorithm		–
maf_parse	Efficient manipulation of large alignments in MAF format		–
msa_view	Manipulation of multiple alignments, including format conversion and extraction of sub alignments	✓	–
phastOdds	Log-odds scoring for phylogenetic models or phylo-HMMs	✓	–
phyloBoot	Parametric and nonparametric bootstrapping for phylogenetic models	✓	–
refeature	Manipulation of genomic features, including format conversion, filtering, grouping	✓	–
tree_doctor	Manipulation of phylogenetic trees, including scaling, pruning, rerooting, relabeling	✓	–

^aCheckmark indicates that majority of functionality is currently supported in RPHAST.