@tskit_dev

Updates from the tree sequence ecosystem.

 Up a tree
tskit.dev
Joined September 2022
  • Tweets18
  • Following21
  • Followers59
8Media
Include

Only show posts containing:

Exclude

Hide posts containing:

Time range
-
Minimum likes
🎉 tskit 0.6.0 is released! 🎉 Thanks to our wonderful contributors, this is a bumper release. Read all about it at: tskit.dev/news/20241106-tski…
7
1
8
514
How to load 1.27 million Covid genomes, and their complex ancestry, into your laptop in ~1 second. If you're into #bioinformatics, help us improve our new software: virological.org/t/towards-pa…

Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2

Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2 Shing H. Zhan1, Anastasia Ignatieva2,3,*, Yan Wong1,*, Katherine Eaton4, Benjamin Jeffery1, Duncan S. Palmer1, Carmen L. Murall4,...

virological.org
1
21
69
15,801
🥳 tskit Python 0.5.5 and C 1.1.2 are released 🥳 This has the excellent random tree seeking by Kevin Thornton which makes hopping to a specific tree much faster. See the full release notes at github.com/tskit-dev/tskit/r…
1
4
134
Tomorrow at 1PM EST I'll be leading an "Intro to stdpopsim" workshop as part of #ProbGen2023. Zoom info attached if ppl would like to join remotely. Join us to learn about this incredible, community resource for simulation
1
16
30
6,724
tskit can make fancy 3D plots for your talks!
Dr Yan Wong@DrYanWong20 Jan 2023
Replying to @tskit_dev
3D tree plots are now easy! tskit.dev/tutorials/viz.html…
3
26
4,084
And finally Python3.11 support means that you can use tskit with the massive performance improvements from Python3.11! (@benjeffery)
1
72
"simplify" now has a "update_sample_flags" option for when you want to manage your own sample nodes. (@jeromekelleher)
1
70
"draw_svg" now has "max_num_trees" to prevent the accidental drawing of thousands of trees, and "canvas_size" for those vertical node labels. (@DrYanWong)
2
1
135
It's now quick and easy to get a tuple of a node's siblings. (@shingheizhan)
1
116
Tree sequences now know their min and max times, based on the nodes and mutations. (@shingheizhan)
1
1
110
Checking if a node was a root could be expensive. No longer with "Tree.is_root" (@DrYanWong)
1
98
🥳 tskit 0.5.4🥳 This first release of the year brings some useful features and support for Python 3.11. Thank you to our lovely community of contributors! github.com/tskit-dev/tskit/r… 🧵👇

Release Python 0.5.4 · tskit-dev/tskit

Features A new Tree.is_root method avoids the need to to search the potentially large list of Tree.roots (@hyanwong, #2669, #2620) The TreeSequence object now has the attributes min_time and ma...

github.com
1
4
8
1,023
We've got a new marketing expert for the tskit ecosystem:
3
12
"The ARG revolution in population and statistical genetics" @WilderWohns talk at @OfficialSMBE is now available at: vimeo.com/759905338/21922bd6…
2
6
tskit-dev retweeted
M Gurke@MarGurke17 Nov 2022
Here is @tskit_dev trying to cheer up their readers. Love it!
1
1
4
🎉tsinfer 0.3.0🎉 This release brings a set of fixes and features, including a substantial improvement in date estimation when tsdate is used after tsinfer 0.3.0. Read all about it here: tskit.dev/news/20221025-tsin…

tskit-dev - Tsinfer 0.3.0!

Tsinfer 0.3.0 introduces a post-processing step that improves time estimation, allows alleles to be listed in any order, and exposes recombination and mismatch ratios to the command-line interface.

tskit.dev
5
1
15
🥳tskit 0.5.3 is released!🥳 Available now on PyPI and conda. This point release contains some fixes and improvements. Full changelog: github.com/tskit-dev/tskit/r… Thank you to all the contributors and the tskit community. ❤️

Release Python 0.5.3 · tskit-dev/tskit

Fixes The Variant object can now be initialized with 64 bit numpy ints as returned e.g. from np.where (@hyanwong, #2518, #2514) Fix tree.mrca for the case of a tree with multiple roots. (@benje...

github.com
5
20
📣"The ARG revolution in population and statistical genetics" 👨‍🏫An invited keynote by @WilderWohns at the SMBEeverywhere symposium. 🗓️Sep 30th at 10am EDT Details here: tskit.dev/news/20220927-smbe…

tskit-dev - Tskit keynote talk

On Fri 30th Sept, an invited talk by Wilder Wohns focussing on results from recent _tskit_-related advances, for the online SMBE Everywhere symposium.

tskit.dev
7
23
Load more