📦 bali-phy

A

• 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 character in its column.✨
• 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.✨

B

• bali-phy(1)Bayesian Inference of Alignment and Phylogeny✨
• bali-phy-pkg(1)Manage BAli-Phy packages✨
• bali-subsample(1)Subsample lines in a file.✨
• bp-analyze(1)Generate an HTML report summarizing bali-phy runs.✨

C

• cut-range(1)Select lines from multiple input files based on lines containing key = value.✨

D

• draw-tree(1)Draw NEWICK (and some other) formatted files.✨

E

• extract-ancestors(1)Extract and name ancestral sequences according to node- and branch- queries.✨

M

• mcon-tool(1)Convert MCON files✨
• mctree-mean-lengths(1)Compute the mean lengths for branches in the given topology.✨
• model_P(1)Compute marginal likelihoods using stabilized harmonic mean estimator✨

P

• pickout(1)Generate table from key = value lines in file.✨

S

• 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.✨

T

• 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)Generate Scaled Regeneration Quantile (SRQ) plot✨