GENOMIC STRUCTURE - Help
Non-redundant
INTRA-INDIVIDUAL VARIATIONS - Help
*In case of slowness, hide the variations to move before displaying them again.
Non-redundant
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
- 2008-CA-053
- Genbank accession number
- SAMN36736055
- Strain
- NA
- Isolate
- OsHV-1/Rivedoux.FRA/2008/Mg-S-053
- Host
- Magallana gigas
- Collection year
- 2008
- Collection date
- Unknown
- Country of origin
- France
- Localisation
- Rivedoux
- Latitude/Longitude
- 46.163,-1.27
- Nature of coordinates
- Unknown
- Host stage
- Juvenil
- Isolation source
- Unknown
- Pool/Individual
- Individual
- Sample conservation method
- Freezer
- Sequencing technology
- Illumina
- Sequencer
- NovaSeq 6000
- Information on sequencing
- Fasteris, 2021
- Number of reads
- Unknown
- Sequence coverage
- Unknown
- Sequence size (BP)
- Unknown
- Pathogen charge
- 125000
- Assembly
- Spades
- Genome type
- Non-redundant
- Structure
- Unknown
- Name of submitter
- Camille Pelletier
- Organization
- Ifremer
- Publication DOI
- TBD
- Notes
- NA
- Number of contigs
- 4