📦 phyx

P

• pxaa2cdn(1)generate codon alignment from aligned amino acids and unaligned nucleotides✨
• pxbdfit(1)fit lineage diversification model to a tree✨
• pxbdsim(1)birth-death tree simulator✨
• pxboot(1)sequence alignment bootstrap or jackknife resampling✨
• pxbp(1)print out bipartitions found in treefiles✨
• pxcat(1)sequence file concatenation✨
• pxclsq(1)clean positions or taxa with too much ambiguous data✨
• pxcltr(1)general tree cleaner✨
• pxcolt(1)collapse edges with support below some threshold✨
• pxcomp(1)sequence compositional homogeneity test✨
• pxconsq(1)compute consensus sequence from an alignment✨
• pxcontrates(1)continuous character rate estimation with Brownian and OU✨
• pxfqfilt(1)filter fastq files by mean quality✨
• pxlog(1)MCMC log file manipulator✨
• pxlssq(1)print sequence file summary✨
• pxlstr(1)print tree summary✨
• pxmono(1)monophyly checker✨
• pxmrca(1)get number of descendant tips of internal nodes by mrca statements✨
• pxmrcacut(1)extract subclades from trees✨
• pxmrcaname(1)label internal nodes with clade names✨
• pxnj(1)basic neighbour-joining tree maker✨
• pxnw(1)conduct Needleman-Wunsch analysis for all the seqs in a file✨
• pxpoly(1)randomly sample polytomies to generate a binary tree✨
• pxrecode(1)nucleotide sequence recoding✨
• pxrevcomp(1)reverse complement sequences✨
• pxrls(1)taxon relabelling from alignments✨
• pxrlt(1)taxon relabelling for trees✨
• pxrmk(1)remove two-degree internal nodes from a tree✨
• pxrms(1)remove sequences by label✨
• pxrmt(1)remove tree tips by label✨
• pxrr(1)reroot (or unroot) a tree file and produce a newick✨
• pxs2fa(1)convert seqfiles from nexus, phylip, fastq to fasta✨
• pxs2nex(1)convert seqfiles from nexus, phylip, or fastq to nexus✨
• pxs2phy(1)convert seqfiles from nexus, phylip, or fastq to phylip✨
• pxseqgen(1)sequence simulator under the GTR model✨
• pxssort(1)sort sequences by id or length✨
• pxsstat(1)calculate multinomial alignment test statistics✨
• pxstrec(1)conduct state reconstruction analyses✨
• pxsw(1)conduct Smith-Waterman analysis for all seqs in a file✨
• pxt2new(1)convert from tree file to newick format✨
• pxt2nex(1)convert from tree file to vanilla Nexus format✨
• pxtcol(1)add information to color edges of a tree✨
• pxtcomb(1)combine set of trees from files✨
• pxtgen(1)generate all tree topologies for n taxa✨
• pxtlate(1)translate DNA alignment to amino acids✨
• pxtrt(1)trace big tree from taxon list and produce newick✨
• pxtscale(1)tree rescaling by factor or root height✨
• pxupgma(1)UPGMA tree generator✨
• pxvcf2fa(1)convert vcf file to fasta✨