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Available VADR model files
Eric Nawrocki edited this page May 7, 2020
·
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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 here, or with some combination of the -m
, -a
,
-i
, -n
, and -x
options. Those options are described more
here.
- See the SARS-CoV-2 instruction page for instructions and example usage.
- FTP page with current model file gzipped tarball
- these models (~30Kb) are larger than the maximum length (25Kb)
allowed by
v-build.pl
and were built with a still in-development version of VADR that is not yet publicly available.
- THIS SET OF MODELS IS INSTALLED WITH VADR (current set is installed with VADR v1.1) and is referred to in the documentation as the "default" set of models
- FTP page with current model file gzipped tarball
- this link will download the specific set of models (vadr-models-1.0-1.tar.gz) used in the manuscript describing VADR v1.0. The construction of the v1.0 set of models is detailed here
- FTP page with current model file gzipped tarball
- see the
00README.txt
file included in the tarball of models for more information and recommendedv-annotate.pl
commands. - 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.