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
- viv48-4-m
- Genbank accession number
- TBD
- Strain
- NA
- Isolate
- NA
- Host
- Magallana gigas
- Collection year
- 2017
- Collection date
- Unknown
- Country of origin
- France
- Localisation
- La floride, La tremblade
- Latitude/Longitude
- 45.803,1.153
- Nature of coordinates
- Unknown
- Host stage
- Spat
- Isolation source
- Gills
- Pool/Individual
- Individual
- Sample conservation method
- Unknown
- Sequencing technology
- Illumina
- Sequencer
- HiSeq 4000
- Information on sequencing
- Unknown
- Number of reads
- Unknown
- Sequence coverage
- Unknown
- Sequence size (BP)
- Unknown
- Pathogen charge
- 19100000
- Assembly
- Spades
- Genome type
- Non-redundant
- Structure
- Unknown
- Name of submitter
- Unknown
- Organization
- Ifremer
- Publication DOI
- https://doi.org/10.3389/fmicb.2021.711377
- Notes
- NA
- Number of contigs
- Unknown