Table 1.

Selected phyx programs and their functions. See github for additional details and full program list

Program	Function
pxlssq/pxlstr	List attributes of alignments/trees
pxrms/pxrmt	Remove taxa from alignments/trees
pxrls/pxrlt	Relabel taxa in alignments/trees
pxboot	Alignment bootstrap/jackknife resampling
pxclsq	Remove missing/ambiguous sites from an alignment
pxs2fa/phy/nex	Convert alignment to fasta/phylip/Nexus format
pxlog	Concatenate and resample MCMC parameter/tree logs
pxfqfilt	Filter fastq files by quality
pxrr	Reroot/unroot trees
pxtlate	Translate nucleotide sequences
pxsw/pxnw	Pairwise sequence alignment
pxstrec	Ancestral state reconstruction, stochastic mapping
pxbdfit/pxbdsim	Birth-death tree inference/simulator
pxseqgen	Simulate nucleotide/protein sequences on user tree