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19 changes: 10 additions & 9 deletions README.md
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Expand Up @@ -29,11 +29,7 @@ resources and [programmatic
tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs)
from the [Open Tree of
Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302)
project: <br/> *Open Tree of Life, Benjamin Redelings, Luna Luisa
Sanchez Reyes, Karen A. Cranston, Jim Allman, Mark T. Holder, & Emily
Jane McTavish. (2019). Open Tree of Life Synthetic Tree (Version 12.3).
Zenodo* doi:
[10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)
project.

You are now on the code repository. Please refer to Physcraper’s
[documentation website](https://physcraper.readthedocs.io/en/latest/)
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If you use Physcraper, please cite:

Sánchez-Reyes, L.L., Kandziora, M. & McTavish, E.J. *Physcraper: a
Python package for continually updated phylogenetic trees using the Open
Tree of Life.* BMC Bioinformatics 22, 355 (2021) doi:
[doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6)
- Sánchez-Reyes, L.L., M. Kandziora, & E.J McTavish. (2021).
*Physcraper: a Python package for continually updated phylogenetic
trees using the Open Tree of Life*. BMC Bioinformatics 22, 355. doi:
[doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6).
<br><br>
- Open Tree of Life, B. Redelings, L.L. Sanchez Reyes, K.A. Cranston,
J. Allman, M.T. Holder, & E.J. McTavish. (2019). *Open Tree of Life
Synthetic Tree (Version 12.3)*. Zenodo. doi:
[10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)

## License

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4 changes: 3 additions & 1 deletion docs/mds/citation.md
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If you use Physcraper, please cite:

Sánchez-Reyes, L.L., Kandziora, M. & McTavish, E.J. *Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.* BMC Bioinformatics 22, 355 (2021) doi: [doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6)
- Sánchez-Reyes, L.L., M. Kandziora, & E.J McTavish. (2021). *Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life*. BMC Bioinformatics 22, 355. doi: [doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6).
<br><br>
- Open Tree of Life, B. Redelings, L.L. Sanchez Reyes, K.A. Cranston, J. Allman, M.T. Holder, & E.J. McTavish. (2019). *Open Tree of Life Synthetic Tree (Version 12.3)*. Zenodo. doi: [10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)
2 changes: 1 addition & 1 deletion docs/mds/intro-header.md
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[![Build Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://travis-ci.org/McTavishLab/physcraper)[![Documentation](https://readthedocs.org/projects/physcraper/badge/?version=latest&style=flat)](https://physcraper.readthedocs.io/en/latest/)[![codecov](https://codecov.io/gh/McTavishLab/physcraper/branch/main/graph/badge.svg)](https://codecov.io/gh/McTavishLab/physcraper)

<img align="right" width="180" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
<img align="right" width="200" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
4 changes: 1 addition & 3 deletions docs/mds/intro.md
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Use a phylogenetic tree and a DNA alignment to automatically find and add nucleotide sequences from a genetic database, to reproducibly improve and advance phylogenetic knowledge in a group.

Physcraper relies on [taxonomic](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3) and [phylogenetic](https://github.com/OpenTreeOfLife/phylesystem-1) resources and [programmatic tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs) from the [Open Tree of Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302) project:
<br/>
*Open Tree of Life, Benjamin Redelings, Luna Luisa Sanchez Reyes, Karen A. Cranston, Jim Allman, Mark T. Holder, & Emily Jane McTavish. (2019). Open Tree of Life Synthetic Tree (Version 12.3). Zenodo* doi: [10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)
Physcraper relies on [taxonomic](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3) and [phylogenetic](https://github.com/OpenTreeOfLife/phylesystem-1) resources and [programmatic tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs) from the [Open Tree of Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302) project.

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