Taxonomy addition for complete trees

Last update: Jun 07, 2022

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Overview

TACT: Taxonomic Addition for Complete Trees

TACT is a Python app for stochastic polytomy resolution. It uses birth-death-sampling estimators across an ultrametric phylogeny to generate branching times for unsampled taxa, using taxonomic information to compatibly place new taxa onto a backbone phylogeny.

Getting started with TACT

Citation

TACT is described more fully in its manuscript. If you use TACT, please cite:

Chang, J., Rabosky, D. L., & Alfaro, M. E. (2019). Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions. Systematic Biology. doi:10.1093/sysbio/syz081

TACT owes its existence to much foundational work in the area of stochastic polytomy resolution, namely PASTIS and CorSiM.

Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. O. (2013). PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences. Methods in Ecology and Evolution, 4(11), 1011–1017. doi:10.1111/2041-210x.12117
Cusimano, N., Stadler, T., & Renner, S. S. (2012). A New Method for Handling Missing Species in Diversification Analysis Applicable to Randomly or Nonrandomly Sampled Phylogenies. Systematic Biology, 61(5), 785–792. doi:10.1093/sysbio/sys031

Sponsorship

Please consider sponsoring the ongoing maintenance of TACT via GitHub Sponsors.

Initial development was supported by a National Science Foundation Doctoral Dissertation Improvement Grant (DEB-1601830).

Comments

dendropy.utility.error.UltrametricityError when using TACT
Hi @jonchang ,

I'm trying to use TACT adding some species to GBMB.tre from Smith and Brown (2018). The backbone is fine, which was confirmed by phyx.

[cactus]$ pxlstr -t GBMB_bi-rmbadtip.tre [some tips are cleaned] tree #: 0 rooted: true binary: true nterminal: 78929 ninternal: 78928 branch lengths: true rttipvar: 2.23112e-10 treelength: 490017 ultrametric: true rootheight: 325.05

When I run TACT with tact_add_taxa function, it gives error as below:

Traceback (most recent call last): File "/home/cactus/.local/bin/tact_add_taxa", line 8, in sys.exit(main()) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(*args, **kwargs) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/tact/cli_add_taxa.py", line 392, in main tree.calc_node_ages() File "/home/cactus/.local/pipx/venvs/tact/lib/python3.7/site-packages/dendropy/datamodel/treemodel.py", line 5666, in calc_node_ages subtree=subtree, dendropy.utility.error.UltrametricityError: Tree is not ultrametric within threshold of 1e-05: 1.0000000017384991e-05. Encountered in subtree of node <Node object at 0x7fc312709470: 'None' (None)> (edge length of 1.291905):

####huge newick tree skipped ...####

Age of children:

<Node object at 0x7fc3127094e0: 'None' (None)>: has age of 88.17562399999998 and edge length of 5.093615, resulting in parent node age of 93.26923899999998

<Node object at 0x7fc3126849b0: 'None' (None)>: has age of 25.721769000000002 and edge length of 67.54748, resulting in parent node age of 93.269249

I suspect it could be issues from dendropy, not really TACT, but would like to hear from your advice first. Thank you!

Happy to mail you my tree file and taxonomy data if you have time to check it.

Cheers,

Miao
opened by Cactusolo 14
Bump scipy from 1.4.1 to 1.5.0
Bumps scipy from 1.4.1 to 1.5.0.

Release notes

Sourced from scipy's releases.

SciPy 1.5.0 Release Notes

SciPy 1.5.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.5.x branch, and on adding new features on the master branch.

This release requires Python 3.6+ and NumPy 1.14.5 or greater.

For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required.

Highlights of this release

wrappers for more than a dozen new LAPACK routines are now available in scipy.linalg.lapack

Improved support for leveraging 64-bit integer size from linear algebra backends

addition of the probability distribution for two-sided one-sample Kolmogorov-Smirnov tests

New features

scipy.cluster improvements

Initialization of scipy.cluster.vq.kmeans2 using minit="++" had a quadratic complexity in the number of samples. It has been improved, resulting in a much faster initialization with quasi-linear complexity.

scipy.cluster.hierarchy.dendrogram now respects the matplotlib color palette

scipy.fft improvements

A new keyword-only argument plan is added to all FFT functions in this module. It is reserved for passing in a precomputed plan from libraries providing a FFT backend (such as PyFFTW and mkl-fft), and it is currently not used in SciPy.

scipy.integrate improvements

Commits

4c0fd79 REL: set version to 1.5.0 "final"

ce8c972 Merge pull request #12391 from tylerjereddy/prep_scipy_150_final

d60c1b3 MAINT: prepare for SciPy 1.5.0 "final"

a7131fa REL: set version to 1.5.0rc2 released

896480b Merge pull request #12345 from tylerjereddy/treddy_150rc2_backports

1e5c8d9 DOC: 1.5.0rc2 release notes update

e468042 CI: don't install pydata/sparse when running on Numpy prerelease

3d96899 CI: split travis arm64 run into two

a3795e9 DOC: update SciPy 1.5.0rc2 release notes

9803615 MAINT: Work around Sphinx bug (#12335)

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dependencies
opened by dependabot[bot] 7
Bump pytest from 5.3.5 to 5.4.0
Bumps pytest from 5.3.5 to 5.4.0.

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c9fd1bd Preparing release version 5.4.0

93aa988 Merge pull request #6901 from RonnyPfannschmidt/regendoc-fix-simple

7996724 Merge pull request #6902 from RoyalTS/filterwarnings-docfix

90ee8a7 docfix

378a75d run and fix tox -e regen to prepare 5.4

e1b3a68 Merge pull request #6896 from nicoddemus/release-trigger

fb7dbc9 Merge pull request #6893 from RonnyPfannschmidt/url-fixes

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dependencies
opened by dependabot-preview[bot] 6
Assumptions made by TACT?

Hi,

I was curious what assumptions TACT means with regards to input files. Occasionally I have noticed that some taxonomically added clades are not monophyletic; for instance, I have a subgenera column, and while this column retains its monophyly, the genera to which subgenera below do not always retain their monophyly when added to the backbone tree.

opened by jsoghigian 4
Bump scipy from 1.8.1 to 1.9.2
Bumps scipy from 1.8.1 to 1.9.2.

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Sourced from scipy's releases.

SciPy 1.9.2 Release Notes

SciPy 1.9.2 is a bug-fix release with no new features compared to 1.9.1. It also provides wheels for Python 3.11 on several platforms.

Authors

Hood Chatham (1)

Thomas J. Fan (1)

Ralf Gommers (22)

Matt Haberland (5)

Julien Jerphanion (1)

Loïc Estève (1)

Nicholas McKibben (2)

Naoto Mizuno (1)

Andrew Nelson (3)

Tyler Reddy (28)

Pamphile Roy (1)

Ewout ter Hoeven (2)

Warren Weckesser (1)

Meekail Zain (1) +

A total of 14 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.9.1 Release Notes

SciPy 1.9.1 is a bug-fix release with no new features compared to 1.9.0. Notably, some important meson build fixes are included.

Authors

Anirudh Dagar (1)

Ralf Gommers (12)

Matt Haberland (2)

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Atsushi Sakai (1)

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A total of 8 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

... (truncated)

Commits

656076c MAINT: wheel push 1.9.2 [wheel build]

ad0d0f9 REL: set 1.9.2 released [wheel build]

d9ad980 Merge pull request #17150 from tylerjereddy/treddy_scipy_192_more_backports

6b098c2 TST: optimize.milp: remove problematic timeout/iteration test

24dce97 DOC: stats.pearsonr: typo in coefficient (#17153)

a6ba7ca MAINT: misc 1.9.2 updates

ed9760e MAINT: stats.pearson3: fix ppf for negative skew (#17055)

6fb6700 FIX: optimize.milp: return feasible solution if available on timeout/node lim...

bcfce27 Merge pull request #17132 from tylerjereddy/treddy_192_backports

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dependencies python
opened by dependabot[bot] 3
Bump scipy from 1.8.1 to 1.9.0
Bumps scipy from 1.8.1 to 1.9.0.

Release notes

Sourced from scipy's releases.

SciPy 1.9.0 Release Notes

SciPy 1.9.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.9.x branch, and on adding new features on the main branch.

This release requires Python 3.8-3.11 and NumPy 1.18.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

We have modernized our build system to use meson, substantially improving our build performance, and providing better build-time configuration and cross-compilation support,

Added scipy.optimize.milp, new function for mixed-integer linear programming,

Added scipy.stats.fit for fitting discrete and continuous distributions to data,

Tensor-product spline interpolation modes were added to scipy.interpolate.RegularGridInterpolator,

A new global optimizer (DIviding RECTangles algorithm) scipy.optimize.direct.

New features

scipy.interpolate improvements

Speed up the RBFInterpolator evaluation with high dimensional interpolants.

Added new spline based interpolation methods for scipy.interpolate.RegularGridInterpolator and its tutorial.

scipy.interpolate.RegularGridInterpolator and scipy.interpolate.interpn now accept descending ordered points.

RegularGridInterpolator now handles length-1 grid axes.

The BivariateSpline subclasses have a new method partial_derivative

... (truncated)

Commits

651a9b7 REL: set 1.9.0 released.

253f894 Merge pull request #16727 from tylerjereddy/treddy_final_190_backports

4e9ed02 REL: 1.9.0 final unreleased.

b83feac DOC: update 1.9.0 relnotes

ee9b834 MAINT: stats.monte_carlo_test: used biased estimate of p-value (#16721)

7ecca8d MAINT: stats: Work around Cython bug. (#16719)

87945b3 DOC: a few mailmap updates

8cefead MAINT: optimize.linprog: ensure integrality can be an array (#16684)

15e96a0 DOC: pin pydata-sphinx-theme to prevent incoming breaking changes.

c4c9348 REL: set 1.9.0rc3 released.

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dependencies python
opened by dependabot[bot] 3
duplicate taxa and error for parenthesis
Hello Jon,

I am using the most recent Docker version of TACT on MacOS and I am trying to add a lot of taxa (16,000) to a relatively sparse (~200) backbone. Maybe this is a bad idea in the first place, which would make sense as to why I'm encountering difficulty. TACT runs fine, but there are a few issues that I am having with the output tree.

There are duplicate taxon names, usually all clustered together away from their taxonomic ranks. Some programs won't open the tree with duplicate taxon names (e.g. FigTree), but others will (e.g. TreeGraph/iTOL).

When I attempt to load the tree into ape/ete3 (with any format option in ete3), I get an error about parenthesis not matching. This is curious since the GUIs seem to open it fine. It doesn't matter which newick format code I use in ete3, I continue to get the error.

It looks like the output tree is not ultrametric, at least how it is displayed in iTOL or TreeGraph. If I export from iTOL it seems to fix the issue with the parentheses, but it is then no longer ultrametric.

Do you have any ideas for these issues? I am happy to send my input files to you via email if that would help.

Many thanks, Paul
opened by pbfrandsen 3
Don't emit rooting annotations for Newick-format trees
The newick tree produced by tact_add_taxa (i.e., *.tacted.newick.tre) has a rooting annotation:

[&R] (newick tree string);

AFAIK such an annotation is not strictly newick-compliant. Regardless, it is giving me trouble with another tool. This PR makes it so that this annotation is not written.
opened by josephwb 3
Bump scipy from 1.8.1 to 1.9.1
Bumps scipy from 1.8.1 to 1.9.1.

Release notes

Sourced from scipy's releases.

SciPy 1.9.1 Release Notes

SciPy 1.9.1 is a bug-fix release with no new features compared to 1.9.0. Notably, some important meson build fixes are included.

Authors

Anirudh Dagar (1)

Ralf Gommers (12)

Matt Haberland (2)

Andrew Nelson (1)

Tyler Reddy (14)

Atsushi Sakai (1)

Eli Schwartz (1)

Warren Weckesser (2)

A total of 8 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.9.0 Release Notes

SciPy 1.9.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.9.x branch, and on adding new features on the main branch.

This release requires Python 3.8-3.11 and NumPy 1.18.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

We have modernized our build system to use meson, substantially improving our build performance, and providing better build-time configuration and cross-compilation support,

Added scipy.optimize.milp, new function for mixed-integer linear

... (truncated)

Commits

2e5883e REL: set 1.9.1 released

fdd33ae Merge pull request #16908 from tylerjereddy/treddy_191_relnotes_update

55e4f9f Update doc/release/1.9.1-notes.rst

04945c5 DOC: 1.9.1 relnotes update

5f06ddd Merge pull request #16904 from rgommers/update-191-pins

987c698 Merge pull request #16901 from tylerjereddy/treddy_191_backports

8e494e1 BLD: update dependency ranges for meson-python and pybind11 for 1.9.1

8b97528 BLD: make the way we count commits for version numbering more robust

cc0a2bf TST: sparse.linalg: Loosen tolerance for the lobpcg test 'test_tolerance_floa...

c055c31 BLD: cp310 needs numpy==1.22.3

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dependencies python
opened by dependabot[bot] 2
Bump ubuntu from 21.04 to 21.10
Bumps ubuntu from 21.04 to 21.10.

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dependencies docker
opened by dependabot[bot] 2
When installing with Linuxbrew: Failed to download resource "tact"
Hi there,

Thanks again for the awesome software!

I've got a working Docker version of TACT on another machine, but I wanted to install TACT on my home WSL machine. But I ran into a problem when trying to install with brew:

myusrname:~$ brew install jonchang/biology/tact ==> Installing tact from jonchang/biology ... (other preqs downloading here) ... ==> Downloading https://dl.bintray.com/jonchang/bottles-biology/tact-0.3.4.x86_64_linux.bottle.tar.gz curl: (22) The requested URL returned error: 403 Forbidden Error: Failed to download resource "tact" Download failed: https://dl.bintray.com/jonchang/bottles-biology/tact-0.3.4.x86_64_linux.bottle.tar.gz

I've truncated the full install messages, because there's just a lot of downloading of other files successfully. I can add them in if you think they might be a problem, but no errors were indicated before attempting to download TACT
opened by jsoghigian 2
Bump scipy from 1.8.1 to 1.9.3
Bumps scipy from 1.8.1 to 1.9.3.

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SciPy 1.9.3 Release Notes

SciPy 1.9.3 is a bug-fix release with no new features compared to 1.9.2.

Authors

Jelle Aalbers (1)

Peter Bell (1)

Jake Bowhay (3)

Matthew Brett (3)

Evgeni Burovski (5)

drpeteb (1) +

Sebastian Ehlert (1) +

GavinZhang (1) +

Ralf Gommers (2)

Matt Haberland (15)

Lakshaya Inani (1) +

Joseph T. Iosue (1)

Nathan Jacobi (1) +

jmkuebler (1) +

Nikita Karetnikov (1) +

Lechnio (1) +

Nicholas McKibben (1)

Andrew Nelson (1)

o-alexandre-felipe (1) +

Tirth Patel (1)

Tyler Reddy (51)

Martin Reinecke (1)

Marie Roald (1) +

Pamphile Roy (2)

Eli Schwartz (1)

serge-sans-paille (1)

ehsan shirvanian (1) +

Mamoru TASAKA (1) +

Samuel Wallan (1)

Warren Weckesser (7)

Gavin Zhang (1) +

A total of 31 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.9.2 Release Notes

SciPy 1.9.2 is a bug-fix release with no new features compared to 1.9.1. It also provides wheels for Python 3.11

... (truncated)

Commits

de80faf REL: set 1.9.3 released [wheel build]

25e6b90 Merge pull request #17239 from tylerjereddy/treddy_backport_193

ba33e43 DOC: update 1.9.3 relnotes

92d892e MAINT: Handle numpy's deprecation of accepting out-of-bound integers.

ba5f6da MAINT: PR 17239 revisions

381089e DOC: update 1.9.3 relnotes

2db3440 BLD: fix invalid shebang for build helper script

a9a6582 DOC: stats.mode: add versionadded tag and correct order of keepdims descripti...

f473888 BLD: fix issue with incomplete threads dependency handling (#17200)

5370f15 MAINT: update meson.build to make it work on IBM i system (#17193)

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dependencies python
opened by dependabot[bot] 0
Bump peaceiris/actions-gh-pages from 3.8.0 to 3.9.0
Bumps peaceiris/actions-gh-pages from 3.8.0 to 3.9.0.

Release notes

Sourced from peaceiris/actions-gh-pages's releases.

actions-github-pages v3.9.0

deps: bump node12 to node16

deps: bump @actions/core from 1.6.0 to 1.10.0

See CHANGELOG.md for more details.

Changelog

Sourced from peaceiris/actions-gh-pages's changelog.

3.9.0 (2022-10-23)

chore

add duplicate (402af2b)

Convert templates to YAML issue forms (ecd92e3)

Disable Bug Report (55635e9)

Fix prettier (#633) (fde6b18), closes #633

fix title (b5022f9)

Fix workflow name (e91a189)

fix year (f2ac8b6)

improve Check list (6a30129)

Improve checklist (69f1241)

Set required to false (d7ab6de)

Set required to false (e8cba38)

update year from 2020 to 2022 (f1f4f15)

ci

add actions/dependency-review-action (3cc0a55)

Add concurrency (edb4f3e)

bump actions/checkout from 2 to 2.3.4 (#610) (3102151), closes #610

bump actions/checkout from 2.3.4 to 2.3.5 (#664) (b19f8b8), closes #664

bump actions/checkout from 2.3.5 to 2.4.0 (#668) (d3d121d), closes #668

bump actions/checkout from 2.4.0 to 3 (#715) (c921422), closes #715

bump actions/dependency-review-action from 1 to 2 (#762) (1304921), closes #762

bump actions/labeler from 3 to 4 (#716) (7954f3d), closes #716

bump actions/setup-node from 2.1.5 to 2.2.0 (#626) (3edcc53), closes #626

bump actions/setup-node from 2.2.0 to 2.3.0 (#632) (69191bf), closes #632

bump actions/setup-node from 2.3.0 to 2.3.1 (#636) (d5e7428), closes #636

bump actions/setup-node from 2.3.1 to 2.3.2 (#637) (4a55c45), closes #637

bump actions/setup-node from 2.3.2 to 2.4.0 (#639) (288fd14), closes #639

bump actions/setup-node from 2.4.0 to 2.4.1 (#656) (52f1a50), closes #656

bump actions/setup-node from 2.4.1 to 2.5.0 (#673) (88eb3e4), closes #673

bump actions/setup-node from 2.5.0 to 2.5.1 (#689) (127e2d7), closes #689

bump actions/setup-node from 2.5.1 to 3 (#713) (c188bee), closes #713

bump actions/upload-artifact from 2 to 3 (#732) (fb2c292), closes #732

bump codecov/codecov-action from 1.5.0 to 1.5.2 (#622) (3087a34), closes #622

bump codecov/codecov-action from 1.5.2 to 2.0.1 (#631) (90e01d5), closes #631

bump codecov/codecov-action from 2.0.1 to 2.0.2 (#634) (d4b79ae), closes #634

bump codecov/codecov-action from 2.0.2 to 2.0.3 (#646) (e363e57), closes #646

bump codecov/codecov-action from 2.0.3 to 2.1.0 (#655) (40515c6), closes #655

bump codecov/codecov-action from 2.1.0 to 3 (#729) (1226087), closes #729

bump codecov/codecov-action from v1.3.1 to v1.3.2 (#594) (1d0fa1a), closes #594

bump codecov/codecov-action from v1.3.2 to v1.4.0 (#602) (b4ccfe8), closes #602

bump codecov/codecov-action from v1.4.0 to v1.4.1 (#604) (e2a2646), closes #604

bump codecov/codecov-action from v1.4.1 to v1.5.0 (#607) (a22219e), closes #607

bump github/codeql-action from 1 to 2 (#739) (cf3948a), closes #739

bump peaceiris/workflows from 0.10.0 to 0.11.0 (#659) (40737e1), closes #659

... (truncated)

Commits

de7ea6f chore(release): 3.9.0

1bf4b35 chore(release): Add build assets

44a2b44 feat: bump node12 to node16 (#791)

2bef62f ci: use actions-github-app-token

2c04d6b ci: bump peaceiris/workflows from 0.16.0 to 0.17.1 (#789)

f2ac8b6 chore: fix year

402af2b chore: add duplicate

e1448a7 docs: bump hugo-version to 0.101.0 (#779)

2eea5d7 ci: drop ubuntu-18.04, add 22.04, latest (#776)

765cf11 docs: add note GitHub official Action

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dependencies github_actions
opened by dependabot[bot] 0

Releases(v0.4.1)

v0.4.1(Aug 3, 2021)
Extreme age ranges when using the Yule or birth-death models now cause fewer optimization issues.

Source code(tar.gz)
Source code(zip)
v0.4.0(Jul 4, 2021)

This minor release of TACT drops support for Python 3.6 (as the latest versions of numpy and scipy have also dropped Python 3.6 support) and introduces the --ultrametricity-precision option to control the precision of ultrametricity checks. The algorithm is similar to the is.ultrametric function in the R package ape. Note that node ages will be normalized be slightly older when the left child and right child's ages differ. See DendroPy's documentation of is_force_max_age for details.
Source code(tar.gz)
Source code(zip)
v0.3.4(Nov 5, 2020)
This release introduces a new dual-optimizer algorithm, which uses simulated annealing to estimate diversification rates when the standard optimizer fails. This should address optimization problems that occur when estimating parameters on particularly species-rich or species-poor groups. It was inspired by prior art in hisse and treePL.

full python 3.9 support since scipy now has cp39 wheels

skip trying to estimate rates for cherries as this never worked to begin with and would always use the ancestor rate anyway

better reporting of which species in the backbone are breaking desired taxonomic monophyly

Source code(tar.gz)
Source code(zip)
v0.3.3(Oct 26, 2020)
update to dendropy 4.5.1

Source code(tar.gz)
Source code(zip)
v0.3.2(Sep 20, 2020)
fixes a numerical precision issue in certain phylogenies with zero length branches

slightly nicer debugging output

dependency updates

Source code(tar.gz)
Source code(zip)
v0.3.1(Jul 15, 2020)
tightens version requirements in anticipation of python 3.9

support docker builds

progress bar is narrower

Source code(tar.gz)
Source code(zip)
v0.3.0(Jul 14, 2020)
Overhauls tact_build_taxonomic_tree in various ways

Now doesn't care if its input is sorted

Will automatically modify non-unique rank names to become unique

Will detect and warn you of empty cells in your taxonomy spreadsheet

Checks that the resultant phylogeny is actually valid

Also turns off a few annoying warnings in tact_add_taxa.
Source code(tar.gz)
Source code(zip)
v0.2.7(Jul 14, 2020)

Fix some DendroPy error messages.
Source code(tar.gz)
Source code(zip)
v0.2.6(Jul 13, 2020)

Tweak build system
Source code(tar.gz)
Source code(zip)
v0.2.5(Jul 8, 2020)
Fix a rare optimization bug when using the Yule model

Fix a rare optimization bug when analysing particularly small phylogenies.

Source code(tar.gz)
Source code(zip)
v0.2.4(Mar 10, 2020)
dependency updates

Source code(tar.gz)
Source code(zip)
v0.2.3(Mar 3, 2020)
tact_add_taxa now correctly restores terminal settings when quitting (https://github.com/jonchang/tact/issues/101)

Source code(tar.gz)
Source code(zip)
v0.2.2(Mar 2, 2020)
tact_add_taxa no longer emits rooting annotations for Newick-format phylogenies (https://github.com/jonchang/tact/pull/98)

Various updates of TACT's dependencies

Source code(tar.gz)
Source code(zip)
v0.2.1(Nov 22, 2019)

This is a patch release for dependency updates.
Source code(tar.gz)
Source code(zip)
v0.2.0(Sep 25, 2019)

This release of TACT adds a --yule option for pure-birth estimations, and also uses arbitrary-precision math in more places to avoid under/overflow errors.
Source code(tar.gz)
Source code(zip)
v0.1.4(Sep 24, 2019)

Source code(tar.gz)
Source code(zip)
v0.1.3(Sep 24, 2019)
migrate to poetry build system

Source code(tar.gz)
Source code(zip)
v0.1.2(Mar 13, 2019)
more bugfixen

Source code(tar.gz)
Source code(zip)
v0.1.1(Mar 13, 2019)
fixes some bugs in tact_build_taxonomy_tree

Source code(tar.gz)
Source code(zip)
v0.1.0(Mar 11, 2019)

Initial release
Source code(tar.gz)
Source code(zip)

Taxonomy addition for complete trees

Related tags

Overview

TACT: Taxonomic Addition for Complete Trees

Getting started with TACT

Citation

Sponsorship

Comments

SciPy 1.5.0 Release Notes

Highlights of this release

New features

scipy.cluster improvements

scipy.fft improvements

scipy.integrate improvements

SciPy 1.9.2 Release Notes

Authors

SciPy 1.9.1 Release Notes

Authors

SciPy 1.9.0 Release Notes

Highlights of this release

New features

scipy.interpolate improvements

SciPy 1.9.1 Release Notes

Authors

SciPy 1.9.0 Release Notes

Highlights of this release

SciPy 1.9.3 Release Notes

Authors

SciPy 1.9.2 Release Notes

actions-github-pages v3.9.0

3.9.0 (2022-10-23)

chore

ci

Releases(v0.4.1)

v0.4.1(Aug 3, 2021)

v0.4.0(Jul 4, 2021)

v0.3.4(Nov 5, 2020)

v0.3.3(Oct 26, 2020)

v0.3.2(Sep 20, 2020)

v0.3.1(Jul 15, 2020)

v0.3.0(Jul 14, 2020)

v0.2.7(Jul 14, 2020)

v0.2.6(Jul 13, 2020)

v0.2.5(Jul 8, 2020)

v0.2.4(Mar 10, 2020)

v0.2.3(Mar 3, 2020)

v0.2.2(Mar 2, 2020)

v0.2.1(Nov 22, 2019)

v0.2.0(Sep 25, 2019)

v0.1.4(Sep 24, 2019)

v0.1.3(Sep 24, 2019)

v0.1.2(Mar 13, 2019)

v0.1.1(Mar 13, 2019)

v0.1.0(Mar 11, 2019)

Owner

Jonathan Chang

Python solutions to Codeforces problems

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Library support get vocabulary from MEM

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Generate a wordlist to fuzz amounts or any other numerical values.

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`scipy.cluster` improvements

`scipy.fft` improvements

`scipy.integrate` improvements

`scipy.interpolate` improvements