Debian 12 (Bookworm) native package

bali-phy

Bayesian Inference of Alignment and Phylogeny

Packages / Debian 12 (Bookworm) / science / bali-phy

Package: bali-phy (3.6.1+dfsg-1)

Maintainers:

Debian Med Packaging Team

External Resources:

Homepage: [www.bali-phy.org]

Bayesian Inference of Alignment and Phylogeny

Other Packages Related to bali-phy:

dep: [libboost-chrono1.74.0] (>= 1.74.0)
C++ representation of time duration, time point, and clocks
dep: [libboost-filesystem1.74.0] (>= 1.74.0)
filesystem operations (portable paths, iteration over directories, etc) in C++
dep: [libboost-program-options1.74.0] (>= 1.74.0)
program options library for C++
dep: [libboost-random1.74.0] (>= 1.74.0)
Boost Random Number Library
dep: [libc6] (>= 2.29)
GNU C Library: Shared libraries
dep: [libcairo2] (>= 1.4.10)
Cairo 2D vector graphics library
dep: [libgcc-s1] (>= 3.4)
GCC support library
dep: [libstdc++6] (>= 9)
GNU Standard C++ Library v3
dep: [perl] [any]
Larry Wall's Practical Extraction and Report Language
dep: [python3]
interactive high-level object-oriented language (default python3 version)

rec: [r-base]
GNU R statistical computation and graphics system
rec: [gnuplot]
Command-line driven interactive plotting program.

sug: [figtree]
graphical phylogenetic tree viewer
sug: [seaview]
Multiplatform interface for sequence alignment and phylogeny

Download bali-phy

Architecture	Package Size	Installed Size	Files
amd64	5.9 MiB	35 MiB	[list of files]
arm64	5.3 MiB	32 MiB	[list of files]

Package file paths (495)

Showing the first 250 sorted package-associated paths. Use file search to locate a specific path.

/usr/bin/alignment-cat
/usr/bin/alignment-chop-internal
/usr/bin/alignment-consensus
/usr/bin/alignment-distances
/usr/bin/alignment-draw
/usr/bin/alignment-find
/usr/bin/alignment-gild
/usr/bin/alignment-indices
/usr/bin/alignment-info
/usr/bin/alignment-max
/usr/bin/alignments-diff
/usr/bin/alignment-thin
/usr/bin/alignment-translate
/usr/bin/bali-phy
/usr/bin/bali-phy-pkg
/usr/bin/bali-subsample
/usr/bin/bp-analyze
/usr/bin/cut-range
/usr/bin/draw-tree
/usr/bin/extract-ancestors
/usr/bin/mctree-mean-lengths
/usr/bin/model_P
/usr/bin/pickout
/usr/bin/statreport
/usr/bin/stats-select
/usr/bin/summarize-ancestors
/usr/bin/tree-mean-lengths
/usr/bin/trees-bootstrap
/usr/bin/trees-consensus
/usr/bin/trees-distances
/usr/bin/trees-to-SRQ
/usr/bin/tree-tool
/usr/lib/bali-phy/Alignment.so
/usr/lib/bali-phy/Alphabet.so
/usr/lib/bali-phy/Array.so
/usr/lib/bali-phy/bindings/distributions/bernoulli.json
/usr/lib/bali-phy/bindings/distributions/beta.json
/usr/lib/bali-phy/bindings/distributions/binomial.json
/usr/lib/bali-phy/bindings/distributions/cauchy.json
/usr/lib/bali-phy/bindings/distributions/exponential.json
/usr/lib/bali-phy/bindings/distributions/gamma.json
/usr/lib/bali-phy/bindings/distributions/geometric.json
/usr/lib/bali-phy/bindings/distributions/iid.json
/usr/lib/bali-phy/bindings/distributions/laplace.json
/usr/lib/bali-phy/bindings/distributions/log_gamma.json
/usr/lib/bali-phy/bindings/distributions/log_laplace.json
/usr/lib/bali-phy/bindings/distributions/log_normal.json
/usr/lib/bali-phy/bindings/distributions/normal.json
/usr/lib/bali-phy/bindings/distributions/poisson.json
/usr/lib/bali-phy/bindings/distributions/shifted_exponential.json
/usr/lib/bali-phy/bindings/distributions/shifted_gamma.json
/usr/lib/bali-phy/bindings/distributions/symmetric_dirichlet.json
/usr/lib/bali-phy/bindings/distributions/symmetric_dirichlet_on.json
/usr/lib/bali-phy/bindings/distributions/uniform_int.json
/usr/lib/bali-phy/bindings/distributions/uniform.json
/usr/lib/bali-phy/bindings/functions/aa.json
/usr/lib/bali-phy/bindings/functions/add.json
/usr/lib/bali-phy/bindings/functions/codons.json
/usr/lib/bali-phy/bindings/functions/constructors/Cons.json
/usr/lib/bali-phy/bindings/functions/constructors/Nil.json
/usr/lib/bali-phy/bindings/functions/cos.json
/usr/lib/bali-phy/bindings/functions/div.json
/usr/lib/bali-phy/bindings/functions/dna.json
/usr/lib/bali-phy/bindings/functions/exp.json
/usr/lib/bali-phy/bindings/functions/getAminoAcids.json
/usr/lib/bali-phy/bindings/functions/getNucleotides.json
/usr/lib/bali-phy/bindings/functions/intToDouble.json
/usr/lib/bali-phy/bindings/functions/length.json
/usr/lib/bali-phy/bindings/functions/letter_pairs.json
/usr/lib/bali-phy/bindings/functions/letters.json
/usr/lib/bali-phy/bindings/functions/log.json
/usr/lib/bali-phy/bindings/functions/map.json
/usr/lib/bali-phy/bindings/functions/mul.json
/usr/lib/bali-phy/bindings/functions/num_branches.json
/usr/lib/bali-phy/bindings/functions/quantile.json
/usr/lib/bali-phy/bindings/functions/replicate.json
/usr/lib/bali-phy/bindings/functions/rna.json
/usr/lib/bali-phy/bindings/functions/sin.json
/usr/lib/bali-phy/bindings/functions/sqrt.json
/usr/lib/bali-phy/bindings/functions/standard_code.json
/usr/lib/bali-phy/bindings/functions/sub.json
/usr/lib/bali-phy/bindings/functions/take.json
/usr/lib/bali-phy/bindings/functions/tan.json
/usr/lib/bali-phy/bindings/functions/uniform_discretize.json
/usr/lib/bali-phy/bindings/functions/unit_mixture.json
/usr/lib/bali-phy/bindings/functions/zip.json
/usr/lib/bali-phy/bindings/functions/zipWith.json
/usr/lib/bali-phy/bindings/models/branch_site.json
/usr/lib/bali-phy/bindings/models/Covarion/galtier01.json
/usr/lib/bali-phy/bindings/models/Covarion/huelsenbeck02.json
/usr/lib/bali-phy/bindings/models/Covarion/ts98.json
/usr/lib/bali-phy/bindings/models/Covarion/wang07.json
/usr/lib/bali-phy/bindings/models/density.json
/usr/lib/bali-phy/bindings/models/dNdS.json
/usr/lib/bali-phy/bindings/models/empirical.json
/usr/lib/bali-phy/bindings/models/equ.json
/usr/lib/bali-phy/bindings/models/f1x4.json
/usr/lib/bali-phy/bindings/models/f3x4.json
/usr/lib/bali-phy/bindings/models/f61.json
/usr/lib/bali-phy/bindings/models/f81.json
/usr/lib/bali-phy/bindings/models/fe.json
/usr/lib/bali-phy/bindings/models/f.json
/usr/lib/bali-phy/bindings/models/fMutSel0.json
/usr/lib/bali-phy/bindings/models/fMutSel.json
/usr/lib/bali-phy/bindings/models/Frequencies/uniform.json
/usr/lib/bali-phy/bindings/models/get_q.json
/usr/lib/bali-phy/bindings/models/gtr.json
/usr/lib/bali-phy/bindings/models/gtr_sym.json
/usr/lib/bali-phy/bindings/models/gwF.json
/usr/lib/bali-phy/bindings/models/gy94_ext.json
/usr/lib/bali-phy/bindings/models/gy94.json
/usr/lib/bali-phy/bindings/models/hky85.json
/usr/lib/bali-phy/bindings/models/hky85_sym.json
/usr/lib/bali-phy/bindings/models/inv.json
/usr/lib/bali-phy/bindings/models/jc69.json
/usr/lib/bali-phy/bindings/models/jtt.json
/usr/lib/bali-phy/bindings/models/k80.json
/usr/lib/bali-phy/bindings/models/lg08_freq.json
/usr/lib/bali-phy/bindings/models/lg08.json
/usr/lib/bali-phy/bindings/models/m1a.json
/usr/lib/bali-phy/bindings/models/m2a.json
/usr/lib/bali-phy/bindings/models/m2a_test.json
/usr/lib/bali-phy/bindings/models/m3.json
/usr/lib/bali-phy/bindings/models/m3_test.json
/usr/lib/bali-phy/bindings/models/m7.json
/usr/lib/bali-phy/bindings/models/m8a.json
/usr/lib/bali-phy/bindings/models/m8a_test.json
/usr/lib/bali-phy/bindings/models/m8.json
/usr/lib/bali-phy/bindings/models/markov_modulate_mixture.json
/usr/lib/bali-phy/bindings/models/mg94_ext.json
/usr/lib/bali-phy/bindings/models/mg94.json
/usr/lib/bali-phy/bindings/models/mg94k.json
/usr/lib/bali-phy/bindings/models/mixture.json
/usr/lib/bali-phy/bindings/models/multiMixtureModel.json
/usr/lib/bali-phy/bindings/models/multi_rate.json
/usr/lib/bali-phy/bindings/models/mut_sel_aa.json
/usr/lib/bali-phy/bindings/models/mut_sel.json
/usr/lib/bali-phy/bindings/models/pam.json
/usr/lib/bali-phy/bindings/models/parameter_mixture.json
/usr/lib/bali-phy/bindings/models/Rates/free.json
/usr/lib/bali-phy/bindings/models/Rates/gamma.json
/usr/lib/bali-phy/bindings/models/Rates/log_normal.json
/usr/lib/bali-phy/bindings/models/rna_16a.json
/usr/lib/bali-phy/bindings/models/rs05.json
/usr/lib/bali-phy/bindings/models/rs07.json
/usr/lib/bali-phy/bindings/models/rs07_relaxed_rates.json
/usr/lib/bali-phy/bindings/models/sample.json
/usr/lib/bali-phy/bindings/models/scaled_mixture.json
/usr/lib/bali-phy/bindings/models/tn93.json
/usr/lib/bali-phy/bindings/models/tn93_sym.json
/usr/lib/bali-phy/bindings/models/wag_freq.json
/usr/lib/bali-phy/bindings/models/wag.json
/usr/lib/bali-phy/bindings/models/x2.json
/usr/lib/bali-phy/bindings/models/x2_sym.json
/usr/lib/bali-phy/bindings/models/x2x2.json
/usr/lib/bali-phy/bindings/models/x3.json
/usr/lib/bali-phy/bindings/models/x3_sym.json
/usr/lib/bali-phy/bindings/models/x3x3.json
/usr/lib/bali-phy/Bits.so
/usr/lib/bali-phy/Char.so
/usr/lib/bali-phy/Data.so
/usr/lib/bali-phy/Distribution.so
/usr/lib/bali-phy/Environment.so
/usr/lib/bali-phy/Foreign.so
/usr/lib/bali-phy/haskell/BAliPhy/ATModel/DataPartition.hs
/usr/lib/bali-phy/haskell/BAliPhy/ATModel.hs
/usr/lib/bali-phy/haskell/Bio/Alignment.hs
/usr/lib/bali-phy/haskell/Bio/Alignment/Matrix.hs
/usr/lib/bali-phy/haskell/Bio/Alignment/Pairwise.hs
/usr/lib/bali-phy/haskell/Bio/Alphabet.hs
/usr/lib/bali-phy/haskell/Bio/Sequence.hs
/usr/lib/bali-phy/haskell/Compiler/Base.hs
/usr/lib/bali-phy/haskell/Compiler/Enum.hs
/usr/lib/bali-phy/haskell/Compiler/IO.hs
/usr/lib/bali-phy/haskell/Compiler/Num.hs
/usr/lib/bali-phy/haskell/Compiler/Real.hs
/usr/lib/bali-phy/haskell/Compiler/ST.hs
/usr/lib/bali-phy/haskell/Control/DeepSeq.hs
/usr/lib/bali-phy/haskell/Control/Monad.hs
/usr/lib/bali-phy/haskell/Data/Array.hs
/usr/lib/bali-phy/haskell/Data/BitVector.hs
/usr/lib/bali-phy/haskell/Data/Bool.hs
/usr/lib/bali-phy/haskell/Data/Char.hs
/usr/lib/bali-phy/haskell/Data/Either.hs
/usr/lib/bali-phy/haskell/Data/Eq.hs
/usr/lib/bali-phy/haskell/Data/Function.hs
/usr/lib/bali-phy/haskell/Data/Ix.hs
/usr/lib/bali-phy/haskell/Data/JSON.hs
/usr/lib/bali-phy/haskell/Data/List.hs
/usr/lib/bali-phy/haskell/Data/Map.hs
/usr/lib/bali-phy/haskell/Data/Matrix.hs
/usr/lib/bali-phy/haskell/Data/Maybe.hs
/usr/lib/bali-phy/haskell/Data/Ord.hs
/usr/lib/bali-phy/haskell/Data/ReadFile.hs
/usr/lib/bali-phy/haskell/Data/Set.hs
/usr/lib/bali-phy/haskell/Data/Text.hs
/usr/lib/bali-phy/haskell/Data/Tuple.hs
/usr/lib/bali-phy/haskell/Foreign/Introspection.hs
/usr/lib/bali-phy/haskell/Foreign/Pair.hs
/usr/lib/bali-phy/haskell/Foreign/String.hs
/usr/lib/bali-phy/haskell/Foreign/Vector.hs
/usr/lib/bali-phy/haskell/IModel.hs
/usr/lib/bali-phy/haskell/MCMC.hs
/usr/lib/bali-phy/haskell/Parameters.hs
/usr/lib/bali-phy/haskell/Parse.hs
/usr/lib/bali-phy/haskell/PopGen.hs
/usr/lib/bali-phy/haskell/Prelude.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Bernoulli.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Beta.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Binomial.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Categorical.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Cauchy.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Dirichlet.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/DirichletProcess.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Discrete.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Exponential.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/ExpTransform.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/FakeDist.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Gamma.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Geometric.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Laplace.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/List.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Mixture.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Normal.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Poisson.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/RandomAlignment.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Tree.hs
/usr/lib/bali-phy/haskell/Probability/Distribution/Uniform.hs
/usr/lib/bali-phy/haskell/Probability.hs
/usr/lib/bali-phy/haskell/Probability/Random.hs
/usr/lib/bali-phy/haskell/Range.hs
/usr/lib/bali-phy/haskell/SMC.hs
/usr/lib/bali-phy/haskell/SModel/Codons.hs
/usr/lib/bali-phy/haskell/SModel/Doublets.hs
/usr/lib/bali-phy/haskell/SModel/Frequency.hs
/usr/lib/bali-phy/haskell/SModel.hs
/usr/lib/bali-phy/haskell/SModel/Likelihood.hs
/usr/lib/bali-phy/haskell/SModel/Nucleotides.hs
/usr/lib/bali-phy/haskell/SModel/ReversibleMarkov.hs
/usr/lib/bali-phy/haskell/System/Environment.hs
/usr/lib/bali-phy/haskell/Tree.hs
/usr/lib/bali-phy/haskell/Tree/Newick.hs
/usr/lib/bali-phy/help/alphabets/Codons.txt
/usr/lib/bali-phy/help/alphabets/Doublets.txt
/usr/lib/bali-phy/help/alphabets/genetic-code.txt
/usr/lib/bali-phy/help/alphabets/Triplets.txt
/usr/lib/bali-phy/help/alphabets.txt
/usr/lib/bali-phy/help/commands/align.txt
/usr/lib/bali-phy/help/commands/alphabet.txt
/usr/lib/bali-phy/help/commands/branch-lengths.txt

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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OpenFactory can boot this operating system in a browser VM, or start a build that includes the native package name from this record.

Try Debian 12 (Bookworm) in the browser Build an image that includes bali-phy

Versions, suites, and repositories

Each row is recorded package-index metadata for one version, architecture, suite, and repository. Names, URLs, and sizes are source-reported; a link is a potentially mutable retrieval location, not an OpenFactory redistribution claim or proof that OpenFactory retained the artifact bytes.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
3.6.1+dfsg-1	bookworm / main	amd64	Debian 12 · main · amd64	5.9 MiB	35 MiB	pool/main/b/bali-phy/bali-phy_3.6.1+dfsg-1_amd64.deb
3.6.1+dfsg-1	bookworm / main	arm64	Debian 12 · main · arm64	5.3 MiB	32 MiB	pool/main/b/bali-phy/bali-phy_3.6.1+dfsg-1_arm64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

Checksums and observation dates

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

3.6.1+dfsg-1 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: e4df62b6a5cbb1b8aa839ec531bf9b108f323fcab292fcd5b4f70be797dda1e6

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'e4df62b6a5cbb1b8aa839ec531bf9b108f323fcab292fcd5b4f70be797dda1e6' 'bali-phy_3.6.1+dfsg-1_amd64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

3.6.1+dfsg-1 / arm64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: 500fbcc2e5c04fe72aee4b4dd6d8fd2de8e6f3a52e643ca6d2275408170bb3b1

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' '500fbcc2e5c04fe72aee4b4dd6d8fd2de8e6f3a52e643ca6d2275408170bb3b1' 'bali-phy_3.6.1+dfsg-1_arm64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified