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Add pointer to f2 from main docs, install, and README #1190

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -9,7 +9,7 @@

![Alt text](funannotate-logo.png?raw=true "Funannotate")

funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at [http://funannotate.readthedocs.io](http://funannotate.readthedocs.io)
funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at <https://funannotate.readthedocs.io>. Since 2025, it has been superseded by funannotate2, see <https://github.com/nextgenusfs/funannotate2> and <https://funannotate2.readthedocs.io>.

#### Quickest start Docker:

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2 changes: 1 addition & 1 deletion docs/index.rst
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Expand Up @@ -26,7 +26,7 @@ Funannotate is a genome prediction, annotation, and comparison software package.

Funannotate is also a lightweight comparative genomics platform. Genomes that have had functional annotation added via the :code:`funannotate annotate` command can be run through the :code:`funannotate compare` script that outputs html based whole genome comparisons. The software can run orthologous clustering, construct whole-genome phylogenies, run Gene Ontology enrichment analysis, as well as calculate dN/dS ratios for orthologous clusters under positive selection.


Here we are describing funannotate version *one*, which has been superceeded since 2025 by version *two*, see `funannotate2 <https://funannotate2.readthedocs.io/>`__.

* :ref:`install`
* :ref:`prepare`
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4 changes: 3 additions & 1 deletion docs/install.rst
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Expand Up @@ -11,7 +11,9 @@ Installation

Funannotate has a lot of dependencies and therefore installation is the most difficult part
of executing the pipeline. The funannotate pipeline is written in python and can be installed
with pip, i.e. `pip install funannotate`. You can see a list of :ref:`dependencies`,
with pip, i.e. `pip install funannotate`. You can see a list of :ref:`dependencies`.

Note here we are describing how to install funannotate version *one*. This was superceeded in 2025 by version *two* where a major goal was to reduce the dependencies to simplify installation, see `funannotate2 <https://funannotate2.readthedocs.io/>`__.

Quickest start Docker:
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