Virus fossil record :
Software downloads :
About this website
This website aims to provide a stable repository for the
virus fossil record. We provide data and bioinformatic tools
for working with the data.
We also post short articles describing our research,
and discussing recent advances in the field of viral evolution.
The website is allied to a bioinformatic 'pipeline' for
screening genome sequences in silico
. Our goal is to
provide a comprehensive fossil record for the reference EVEs
in our libraries by creating MSAs that incorporate all
homologous loci identified by screening.
The EVE reference sequence libraries
We provide paleovirus reference sequences for retroviruses
Reference sequences for non-retroviral paleoviruses will be provided
in the near future.
Our reference sequences are provided in our native format (GLUE)
and also as FASTA sequences.
The current version of the ERV reference sequence library
(2013-05-25) is a development version
that is under consolidation during April 2013.
It includes previously published consensus sequences, as well as
'reference' loci/isolates selected to represent particular retroviral
Our ultimate goal is to provide estimated ancestral sequences for
ERV lineages that have sufficiently high copy number.
Representing the fossil history of EVE lineages
Our approach to organization of the sequence data that comprise the
virus fossil record is based on the use of a framework developed in our
inked by their U
In the GLUE framework, multiple sequence alignments (MSAs) are
generated against standard 'reference sequences', and the positions and
sequences of insertions relative to the reference sequence
are spliced out and stored in tables.
This approach expedites the progressive assembly of paleovirus MSAs,
and circumvents many of the problems encountered when MSAs contain
pseudogenes and large indels.