view clipkit_repo/docs/other_software/index.rst @ 0:49b058e85902 draft

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

.. _other_software:


Other software
==============

^^^^^

We are grateful that you are exploring our software! If this software is of interest 
to you, our other software will likely be too. Please see other software below.

|

PhyKIT
------
|PhyKIT|

A broadly applicable command line toolkit with 30 (and counting) functions for analyzing
and processing phylogenetic trees and multiple sequence alignments.

`Publication PDF <https://jlsteenwyk.com/publication_pdfs/2021_Steenwyk_etal_Bioinformatics.pdf>`_;
`Documentation <https://jlsteenwyk.com/PhyKIT/>`_;
`Source code <https://github.com/JLSteenwyk/PhyKIT>`_

.. |PhyKIT| image:: ../_static/img/phykit_logo.png
   :width: 50%

|

orthofisher
-----------
|orthofisher|

automated extraction of protein sequences from proteomes using profile Hidden Markov Models

`Documentation <https://jlsteenwyk.com/orthofisher/>`_;
`Source code <https://github.com/JLSteenwyk/orthofisher>`_

.. |orthofisher| image:: ../_static/img/orthofisher_full_logo.jpg
   :width: 50%

|

treehouse
---------

|treehouse|

prune user inputted phylogenies or phylogenies in our database using an intuitive graphical
user interface.

`Publication PDF <https://jlsteenwyk.com/publication_pdfs/2019_Steenwyk_and_Rokas_BMC_Research_Notes.pdf>`_;
`Documentation & Source code <https://github.com/JLSteenwyk/treehouse>`_

.. |treehouse| image:: ../_static/img/treehouse_logo.png
   :width: 50%

|

ggpubfigs
---------

|ggpubfigs|

create publication ready figures that are colorblind friendly using our collection of ggplot2 themes

`Zenodo record <https://zenodo.org/record/4126988#.YCK_2ZNKhlc>`_;
`Documentation & Source code <https://github.com/JLSteenwyk/ggpubfigs>`_

.. |ggpubfigs| image:: ../_static/img/ggpubfigs_logo.png
   :width: 50%