Bali-Phy

• alignment-cat(1) \f[B]alignment-cat\f[R] - Concatenate several alignments (with the same sequence names) end-to-end.
• alignment-chop-internal(1) \f[B]alignment-chop-internal\f[R] - Remove ancestral sequences from an alignment.
• alignment-consensus(1) \f[B]alignment-consensus\f[R] - Construct a consensus alignment to summarize an alignment sample.
• alignment-distances(1) \f[B]alignment-distances\f[R] - Compute distances between alignments.
• alignment-draw(1) \f[B]alignment-draw\f[R] - Draw an alignment to HTML, optionally coloring residues by AU.
• alignment-find(1) \f[B]alignment-find\f[R] - Find the last (or first) FASTA alignment in a file.
• alignment-gild(1) \f[B]alignment-gild\f[R] - Annotate each residue in the alignment according to the probability that it should align to the hypothetical root
• alignment-indices(1) \f[B]alignment-indices\f[R] - Show the alignment in terms of the index of each character in its sequence.
• alignment-info(1) \f[B]alignment-info\f[R] - Show useful statistics about the alignment.
• alignment-max(1) \f[B]alignment-max\f[R] - Construct a posterior decoding alignment to summarize an alignment sample.
• alignment-thin(1) \f[B]alignment-thin\f[R] - Remove sequences or columns from an alignment.
• alignment-translate(1) \f[B]alignment-translate\f[R] - Translate a DNA/RNA alignment into amino acids.
• alignments-diff(1) \f[B]alignments-diff\f[R] - Align two alignments for comparison.
• bali-phy-pkg(1) \f[B]bali-phy-pkg\f[R] - Manage BAli-Phy packages
• bali-phy(1) \f[B]bali-phy\f[R] - Bayesian Inference of Alignment and Phylogeny
• bali-subsample(1) \f[B]subsample\f[R] - Subsample lines in a file.
• bp-analyze(1) \f[B]bp-analyze\f[R] - Generate an HTML report summarizing bali-phy runs.
• cut-range(1) \f[B]cut-range\f[R] - Select lines between certain values of a key. (e. iterations)
• draw-tree(1) \f[B]draw-tree\f[R] - Draw NEWICK (and some other) formatted files.
• extract-ancestors(1) \f[B]extract-ancestors\f[R] - Extract and name ancestral sequences according to node- and branch- queries.
• mctree-mean-lengths(1) \f[B]tree-mean-lengths\f[R] - Compute the mean lengths for branches in the given topology.
• model_P(1) \f[B]model_P\f[R] - Compute marginal likelihoods using stabilized harmonic mean estimator
• pickout(1) \f[B]pickout\f[R] - Generate table from key = value lines in file.
• statreport(1) \f[B]statreport\f[R] - Compute summary statistics for tab-delimited data files.
• stats-select(1) \f[B]stats-select\f[R] - Select columns from a Tracer-format data file.
• summarize-ancestors(1) \f[B]summarize-ancestors\f[R] - Construct alignments with internal sequences for labeled nodes in query tree.
• tree-mean-lengths(1) \f[B]tree-mean-lengths\f[R] - Compute the mean lengths for branches in the given topology.
• tree-tool(1) \f[B]tree-tool\f[R] - Perform various operations on Newick trees.
• trees-bootstrap(1) \f[B]trees-bootstrap\f[R] - Compare support for partitions between different files.
• trees-consensus(1) \f[B]trees-consensus\f[R] - Find consensus trees and supported splits.
• trees-distances(1) \f[B]trees-distances\f[R] - Compute autocorrelations or other functions of tree distances.
• trees-to-SRQ(1) \f[B]tree-to-srq\f[R] - Generate Scaled Regeneration Quantile (SRQ) plot