There are no visualisations available for the following files:
- Variations file (VCF)
GENOMIC STRUCTURE - Help
Complete
PHYLOGENETIC PLACEMENT - Help
jModeltest 2.1.10 command : -tr 56 -d alignment.phy -s 3 -i -g 8 -f -AIC -o jmodeltest.out
Best model : HKY+I+G
Phyml 20130103 command : phyml -i alignment.phy -d nt -n 1 -b 0 --run_id HKY+I+G -m 010010 -f m -v e -c 8 -a e --no_memory_check -o tlr -s BEST
The phylogeny is done with the non-redundant sequences when possible because a structure similarity is needed.
Better visualisation and more interactive phylogeny of Ostreid herpesvirus-1 here.
METADATA
*TBD : To Be Determined; NA : Non-applicable
- Sample name
- KY242785
- Genbank accession number
- KY242785
- Strain
- NA
- Isolate
- microVar variant A
- Host
- Magallana gigas
- Collection year
- 2010
- Collection date
- June 10, 2010
- Country of origin
- France
- Localisation
- Unknown
- Latitude/Longitude
- 46.603354,1.8883335
- Nature of coordinates
- Approximated
- Host stage
- Spat
- Isolation source
- Mantle_Gills
- Pool/Individual
- Pool
- Sample conservation method
- -80°C
- Sequencing technology
- Illumina
- Sequencer
- NextSeq 500
- Information on sequencing
- Unknown
- Number of reads
- Unknown
- Sequence coverage
- Unknown
- Sequence size (BP)
- Unknown
- Pathogen charge
- Unknown
- Assembly
- Mapping Bowtie2
- Genome type
- Complete and Non-redundant
- Structure
- TRL-UL-IRL-X-IRS-US-TRS-X and UL-IRL-X-IRS-US
- Name of submitter
- Unknown
- Organization
- Unknown
- Publication DOI
- 10.1016/j.virol.2017.06.027
- Notes
- NA
- Number of contigs
- Unknown