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