Mercurial > repos > padge > clipkit
diff clipkit_repo/docs/about/index.rst @ 0:49b058e85902 draft
"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author | padge |
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date | Fri, 25 Mar 2022 13:04:31 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clipkit_repo/docs/about/index.rst Fri Mar 25 13:04:31 2022 +0000 @@ -0,0 +1,163 @@ +About +===== + +^^^^^ + +**Clip**\ing and **K**\eeping **I**\nformation **T**\rimmer (**ClipKIT**) was developed as +part of `Jacob L. Steenwyk <https://jlsteenwyk.github.io/>`_'s graduate thesis work. + +Since the early 1990's, multiple sequence alignments have been filtered or "trimmed" +to remove sites that may cause errors in phylogenetic inference. Errors can be caused by +erroneously inferring site homology or saturation of multiple substitutions, both of which +often present as highly divergent sites. However, recent analysis by |TanLink|_ revealed +current methods of alignment trimming often resulted in worse phylogenetic inferences. +These findings highlight the need for alternative MSA trimming strategies. + +In light of these findings, we developed ClipKIT, which implements an innovative yet simple +trimming strategy. ClipKIT achieves this by identifying and retaining phylogenetically-informative +sites rather than identifying and trimming highly divergent ones. Our assessments of ClipKIT's +performance using empirical datasets of Mammalian and Yeast sequences and simulated sequences +from metazoans, flowering plants, filamentous fungi, and budding yeasts (:ref:`see details here +<performance>`) suggests ClipKIT is a top-performing software. + +.. _TanLink: https://academic.oup.com/sysbio/article/64/5/778/1685763 +.. |TanLink| replace:: Tan *et al.* (2015) + +| + +The Developers +-------------- + +^^^^^ + +ClipKIT is developed and maintained by `Jacob L. Steenwyk <https://jlsteenwyk.github.io/>`_ +and `Thomas J. Buida III <www.tjbiii.com>`_. + +| + +|JLSteenwyk| + +|GoogleScholarSteenwyk| |GitHubSteenwyk| |TwitterSteenwyk| + +`Jacob L. Steenwyk <https://jlsteenwyk.github.io/>`_ is a Howard Hughes Medical Institute +Gilliam fellow in the `Antonis Rokas Laboratory <https://as.vanderbilt.edu/rokaslab/>`_ at +`Vanderbilt University <https://www.vanderbilt.edu/>`_. His research foci include understanding +the parameters that influence genome stability, the genomics of microbial domestication, and +the evolution of pathogenicity. Beyond research, Steenwyk aims to make education more accessible +through diverse avenues of community engagement. Find out more information at his +`personal website <http://jlsteenwyk.github.io/>`_. + +.. |JLSteenwyk| image:: ../_static/img/Steenwyk.jpg + :width: 35% + +.. |GoogleScholarSteenwyk| image:: ../_static/img/GoogleScholar.png + :target: https://scholar.google.com/citations?user=VXV2j6gAAAAJ&hl=en + :width: 4.5% + +.. |TwitterSteenwyk| image:: ../_static/img/Twitter.png + :target: https://twitter.com/jlsteenwyk + :width: 4.5% + +.. |GitHubSteenwyk| image:: ../_static/img/Github.png + :target: https://github.com/JLSteenwyk + :width: 4.5% + +| + +|TJBuida| + +|GitHubBuida| |TwitterBuida| + +`Thomas J. Buida III <http://tjbiii.com/>`_ is a senior software and data engineer at +`Initial State <https://www.initialstate.com/>`_. His main interests are in the +design and execution of elegant solutions to complex data problems. His expertise lies +in backend software development. Flagship side projects include `twitch-top-eight +<https://github.com/TJBIII/twitch-top-eight>`_, a panel +extension to view top viewers/streamers, and `Hue Kolorize +<https://github.com/TJBIII/hue-kolorize>`_, a Hue light extension that matches the dominant +color extracted from a flexible source to the Hue light color. Find out more information at his +`personal website <http://tjbiii.com/>`_. + + +.. |TJBuida| image:: ../_static/img/Buida.jpeg + :width: 35% + +.. |TwitterBuida| image:: ../_static/img/Twitter.png + :target: https://twitter.com/thomasbuida + :width: 4.5% + +.. |GitHubBuida| image:: ../_static/img/Github.png + :target: https://github.com/TJBIII + :width: 4.5% + +| + +More Team Members +----------------- + +^^^^^ + +ClipKIT has been made possible by other key personnel including `Antonis Rokas +<https://as.vanderbilt.edu/rokaslab/>`_, Yuanning Li, and `Xing-Xing +Shen <https://xingxingshen.github.io/>`_. + +| + +|ARokas| + +|GoogleScholarRokas| |TwitterRokas| + +`Antonis Rokas <https://as.vanderbilt.edu/rokaslab/>`_ is the Cornelius Vanderbilt Chair in +Biological Sciences and Director of the `Evolutionary Studies Initiative +<https://www.vanderbilt.edu/evolution/>`_ at `Vanderbilt University <https://www.vanderbilt.edu/>`_. +Research in his laboratory focuses on the study of the DNA record to gain insight into the patterns and +processes of evolution. Using a combination of computational and experimental approaches, his lab’s current +research aims to understand the molecular foundations of the fungal lifestyle, the reconstruction of the +tree of life, and the evolution of human pregnancy. Find out more information at his +`laboratory’s website <https://as.vanderbilt.edu/rokaslab/>`_. + +.. |ARokas| image:: ../_static/img/Rokas.jpeg + :width: 35% + +.. |GoogleScholarRokas| image:: ../_static/img/GoogleScholar.png + :target: https://scholar.google.com/citations?user=OvAV_eoAAAAJ&hl=en + :width: 4.5% + +.. |TwitterRokas| image:: ../_static/img/Twitter.png + :target: https://twitter.com/RokasLab + :width: 4.5% + +| + +|XXShen| + +|GoogleScholarShen| |GitHubShen| |TwitterShen| + +`Xing-Xing Shen <https://xingxingshen.github.io/>`_ is an Assistant Professor of Institute of +Insect Sciences at Zhejiang University. His lab is broadly interested in evolutionary biology, +phylogenetics, comparative genomics, and bioinformatics. His current research mainly focus on: +1) investigating phylogenetic relationships in animals and fungi using genome-scale data; +2) identifying the factors that lead to phylogenetic incongruence; +and 3) exploring insect species and ecological diversity. Find out more information at his +`laboratory's website <https://xingxingshen.github.io/>`_. + +.. |XXShen| image:: ../_static/img/Shen.jpg + :width: 35% + +.. |GoogleScholarShen| image:: ../_static/img/GoogleScholar.png + :target: https://scholar.google.com/citations?user=aNqPBsEAAAAJ&hl=en + :width: 4.5% + +.. |TwitterShen| image:: ../_static/img/Twitter.png + :target: https://twitter.com/shenxingxing1 + :width: 4.5% + +.. |GitHubShen| image:: ../_static/img/Github.png + :target: https://github.com/xingxingshen + :width: 4.5% + +| + +Information about other team members coming soon! + +