From 5cbc7e35d92bcff22117d910a274db9dc92f4596 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Tue, 4 Aug 2026 12:20:35 +0100 Subject: [PATCH] Add pointer to f2 from main docs, install, and README --- README.md | 2 +- docs/index.rst | 2 +- docs/install.rst | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index dd3573e8..bc472288 100644 --- a/README.md +++ b/README.md @@ -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 . Since 2025, it has been superseded by funannotate2, see and . #### Quickest start Docker: diff --git a/docs/index.rst b/docs/index.rst index 70281f4a..9d088646 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -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 `__. * :ref:`install` * :ref:`prepare` diff --git a/docs/install.rst b/docs/install.rst index 2793c997..fa9886e3 100644 --- a/docs/install.rst +++ b/docs/install.rst @@ -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 `__. Quickest start Docker: ----------------------