You can download pre-built models to use to validate and annotate
virus sequences or cox1 gene sequences as listed
below. ***Importantly***, to use a set of models other than the
default set that is installed with VADR, you will need to use either
the `--mdir` and `--mkey` options to `v-annotate.pl` as shown in the
SARS-CoV-2 example on this [page](https://github.com/ncbi/vadr/wiki/Coronavirus-annotation), or with some combination of the `-m`, `-a`,
`-i`, `-n`, and `-x` options. Those options are described more
[here](https://github.com/ncbi/vadr/blob/master/documentation/annotate.md#v-annotatepl-options-related-to-model-files).

---
Models developed at NLM/NCBI:

* [SARS-CoV-2 and other *Coronaviridae* RefSeq models](#corona)
* [Influenza models](#flu)
* [Mpox virus (MPXV) RefSeq model](#mpxv)
* [RSV models](#rsv)
* [Norovirus and other *Caliciviridae* RefSeq models](#calici)
* [Dengue virus and other *Flaviviridae* RefSeq models](#flavi)
* [Metazoan Cytochrome c oxidase I (COX1) models models](#cox1)

Models developed in collaboration with the Greninger Lab, Univ of Washington:

* [Hepatitis A virus (HAV) models](#hav)
* [Measles virus (MeV) models](#mev)
* [Mumps virus (MuV) models](#muv)
* [Rubella virus (RuV) models](#ruv)
* [Seasonal human coronavirus (HCoV) models](#hcov)
* [Human parainfluenza (HPIV) models](#hpiv)
* [Human metapneumovirus (HMPV) models](#hmpv)
* [Herpes Simplex Virus (HSV-1 and HSV-2) models](#hsv)

---
## <a name="corona"></a>**SARS-CoV-2 and other *Coronaviridae* RefSeq VADR models**

* See the [SARS-CoV-2 instruction page](https://github.com/ncbi/vadr/wiki/Coronavirus-annotation) for instructions and example usage.
* [FTP page with current SARS-CoV-2 model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/sarscov2/CURRENT)
* [FTP page with current *Coronaviridae* model file (includes current SARS-CoV-2 models) gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/coronaviridae/CURRENT)
* [SARS-CoV-2 model bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-sarscov2) (includes set 1.2-1 (March 2021) and later)
* [*Coronaviridae* model bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-corona) (includes set 1.2-1 (March 2021) and later)
---
## <a name="flu"></a>**Influenza virus (flu) VADR models**

* See the [flu instruction page](https://github.com/ncbi/vadr/wiki/Influenza-annotation) for instructions and example usage.
* [FTP page with current flu model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/flu/CURRENT)
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-flu) for these models

---
## <a name="mpxv"></a>**Mpox virus (MPXV) RefSeq VADR models**

* See the [Mpox virus instruction page](https://github.com/ncbi/vadr/wiki/Mpox-virus-annotation) for instructions and example usage.
* [FTP page with current MPXV model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/mpxv/CURRENT)
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-mpxv) for these models

---
## <a name="rsv"></a>**Respiratory syncytial virus (RSV) VADR models**

* See the [RSV instruction page](https://github.com/ncbi/vadr/wiki/RSV-annotation) for instructions and example usage.
* [FTP page with current RSV model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/rsv/CURRENT)
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-rsv) for these models
* [A tutorial on building an RSV model library](https://github.com/ncbi/vadr/blob/master/documentation/advbuild.md#top)

---
## <a name="calici"></a>**Norovirus and other *Caliciviridae* RefSeq VADR models**
* ***THIS SET OF MODELS IS INSTALLED WITH VADR*** (current set is installed with VADR v1.3) and is referred
  to in the documentation as the "default" set of models
* these models are currently used to validate and annotate incoming Norovirus sequence submissions to GenBank
  using the following options:

  ```
  v-annotate.pl --split --cpu 1 --group Norovirus --nomisc --noprotid <fasta-file-to-annotate> <output-directory-to-create>
  ```

* ***Previously*** (v 1.1.3 and earlier) the default set of models included both *Caliciviridae* and *Flaviviridae* models, but 
  as of v1.2 they are split into two model sets, although both are installed by the VADR installation script.
* [FTP page with current model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/caliciviridae/CURRENT)
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-calici) for these models (includes set 1.2-1 (March 2021) and later)
* [this link](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/CURRENT/vadr-models-1.0-1.tar.gz)
  will download the specific set of models
  (vadr-models-1.0-1.tar.gz) used in the [manuscript describing VADR
  v1.0](https://www.biorxiv.org/content/10.1101/852657v1). The construction of the v1.0 set of models is detailed
  [here](https://github.com/ncbi/vadr/blob/vadr-1.0/documentation/build.md#how-the-vadr-10-model-library-was-constructed-)

---
## <a name="flavi"></a>**Dengue virus and other *Flaviviridae* RefSeq VADR models**
* ***THIS SET OF MODELS IS INSTALLED WITH VADR*** (current set is installed with VADR v1.2)  to in the documentation as the "default" set of models
* these models are currently used to validate and annotate incoming Dengue virus sequence submissions to GenBank
  using the following options:

  ```
  v-annotate.pl --split --cpu 1 --group Dengue --nomisc --noprotid --mkey flavi <fasta-file-to-annotate> <output-directory-to-create>
  ```

* ***Previously*** (v 1.1.3 and earlier) the default set of models included both *Caliciviridae* and *Flaviviridae* models, but 
  as of v1.2 they are split into two model sets, although both are installed by the VADR installation script.
  To use the *Flaviviridae* model set, you'll need to use the `--mkey flavi` option with `v-annotate.pl`.
* [FTP page with current model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/flaviviridae/CURRENT)
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-flavi) for these models (includes set 1.2-1 (March 2021) and later)

---

## <a name="hav"></a>**Hepatitis A virus (HAV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for HAV see the Greninger lab [HAV model github repo](https://github.com/greninger-lab/vadr-models-hav).

---

## <a name="mev"></a>**Measles virus (MeV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for MeV see the Greninger lab [MeV model github repo](https://github.com/greninger-lab/vadr-models-mev).

---

## <a name="muv"></a>**Mumps virus (MuV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for MuV see the Greninger lab [MuV model github repo](https://github.com/greninger-lab/vadr-models-muv).

---

## <a name="ruv"></a>**Rubella virus (RuV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for RuV see the Greninger lab [RuV model github repo](https://github.com/greninger-lab/vadr-models-ruv).

---

## <a name="hcov"></a>**Seasonal human coronavirus (HCoV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for HCoV see the Greninger lab [HCoV model github repo](https://github.com/greninger-lab/vadr-models-hcov).

---

## <a name="hpiv"></a>**Human parainfluenza virus (HPIV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for HPIV see the Greninger lab [HPIV model github repo](https://github.com/greninger-lab/vadr-models-hpiv).
 
---

## <a name="hmpv"></a>**Human metapneumovirus (HMPV) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jeffrey Furlong and Stephanie Goya in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for HMPV see the Greninger lab [HMPV model github repo](https://github.com/greninger-lab/vadr-models-hmpv).

---
## <a name="hsv"></a>**Herpes Simplex Virus (HSV-1 and HSV-2) models, from the Greninger Lab, Univ of Washington**
* These models were created by Jaydee Sereewit (HSV-1) and Jeffrey Furlong (HSV-2) in Alex Greninger's lab at University of Washington, Seattle.
* For instructions on downloading and using these models for HSV-1 or HSV-2 annotation see the Greninger lab [HSV model github repo](https://github.com/greninger-lab/vadr-models-hsv).

---

## <a name="cox1"></a>**Metazoan Cytochrome c oxidase I (COX1) VADR models**
* [FTP page with current model file gzipped tarball](https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/cox1/CURRENT)
* these models are currently used to validate and annotate incoming cox1 (nucleotide) sequence submissions to GenBank
  using the following options:

  ```
  v-annotate.pl --split --cpu 4 --xmaxdel 3 --xmaxins 3 --xlongest --mkey cox1 --alt_pass lowcovrg --alt_fail fstlocfi,fstlocf5,fstlocf3 --fstminnti 5 --fstminnt5 5 --fstminnt3 5 --nomisc --noprotid --xsub <cox1-models-dir-path>/cox1.phy.xsub --mdir <cox1-models-dir-path> <fasta-file-to-annotate> <output-directory-to-create>
  ```

* see the `00README.txt` file included in the tarball of models for more
  information and recommended `v-annotate.pl` commands.
* [Bitbucket repo](https://bitbucket.org/nawrockie/vadr-models-cox1) for these models (includes set 1.2-1 (March 2021) and later)
* these models are currently in testing for analyzing metazoan cox1
  sequence submissions to GenBank
* these models were built from alignments instead of single
  RefSeqs. The alignments are included in Stockholm format in the tarballs as `.stk` files.
      
---
#### Questions, comments, feature or model requests? Send a mail to eric.nawrocki@nih.gov.