Taxonomy addition for complete trees

Related tags

Miscellaneous python
Overview

TACT: Taxonomic Addition for Complete Trees

PyPI Build status Docker Hub

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

    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

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    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

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    scipy.integrate improvements

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    dependencies 
    opened by dependabot[bot] 7
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    dependencies 
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  • Assumptions made by TACT?

    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

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    ... (truncated)

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

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    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)

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    • 7ecca8d MAINT: stats: Work around Cython bug. (#16719)
    • 87945b3 DOC: a few mailmap updates
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    dependencies python 
    opened by dependabot[bot] 3
  • duplicate taxa and error for parenthesis

    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.

    1. 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).
    2. 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.
    3. 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

    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

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    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)

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    dependencies python 
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    dependencies docker 
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  • When installing with Linuxbrew: Failed to download resource

    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

    Bump scipy from 1.8.1 to 1.9.3

    Bumps scipy from 1.8.1 to 1.9.3.

    Release notes

    Sourced from scipy's releases.

    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)
    • Additional commits viewable in compare view

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

    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

    ci

    ... (truncated)

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    dependencies github_actions 
    opened by dependabot[bot] 0
Releases(v0.4.1)
Owner
Jonathan Chang
I am an evolutionary biologist whose research involves understanding the origin and maintenance of biological diversity.
Jonathan Chang
GitHub https://tact.jonathanchang.org
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