annotate clipkit_repo/docs/about/index.rst @ 0:49b058e85902 draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

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!