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. 2017 Feb 8;33(12):1886–1888. doi: 10.1093/bioinformatics/btx063

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