tbas-history

T-BAS v1 features

Single-locus placement of unknown taxa sequences and user-customizable metadata on two included trees: fungi (Ascomycota) and bacteria
Single-locus placement on a user-provided reference tree, multi-locus sequence alignments and metadata
Option to select from two phylogeny-based placement options: EPA and backbone constraint tree
Classification of unknown nrITS barcode sequences using the UNITE fungal nrITS database
Metadata displayed as colorized outer rings in phylogenies
Save trees and color legends as SVG, PNG or PDF files

Multi-locus placement of unknown taxa sequences with user-customizable metadata on eleven included reference trees
Multi-locus placement on user-uploaded reference tree, multi-locus sequence alignments and metadata
Standardization of phylogenetic placement and metadata output using the extended PhyloXML format
Perform cumulative placement of unknown taxa sequences on reference tree
Pre-filtering and/or classification of unknown nrITS or 16S rDNA barcode sequences using the UNITE fungal nrITS database or SILVA bacterial database
Option to select from three phylogeny-based placement options: EPA, backbone constraint tree, and de novo phylogenetic reconstruction using RAxML
Option to select specific clades and perform phylogenetic inference across single or multiple alignments with RAxML or network inference using TCS and NetworkX
Color editor for synchronizing color-coded attributes across subtrees and networks
Display metadata as colorized outer rings in phylogenies
Display network graphs with node attributes
Save trees, networks and color legends as SVG, PNG or PDF files

2019-01-01 Update html on Upload Tree page
2019-01-14 Add 7th box for custom placement
2019-01-29 Add zoom icon to rectangular layout
2019-01-29 Change Mafft version from MAFFT_TG to MAFFT_XSEDE
2019-02-04 Add toggle view bands 4-12
2019-02-06 Add, update controls for font size and bootstrap font size
2019-02-15 Update data for Rhizoctonia
2019-02-19 Add code to upload page to check user has permisison to place on selected tree and also update table on the server to associate run number with placement tree. This data is checked when viewing a tree to ensure only users with permisison can view restricted trees.
2019-03-05 Add link and page to submit a placement as a submitted tree.
2019-03-13 Add option on Upload Tree page for user to customize the BLAST UNITE filter.
2019-03-14 Add functionality to place on user submitted trees.
2019-03-16 Add Laboulbeniomycetes tree
2019-03-22 Add report to show difference in metadata and tree names.
2019-04-16 Add small number to branch lengths to display trees submitted with zero branch length.
2019-04-26 Add bands to rectangular display up to 12 bands
2019-04-29 Allow user to select tree download as phylip or nexus
2019-05-01 Re-write Update Attributes page to allow user to download csv of current attributes, edit, and upload for changes.
2019-05-07 New Xylariales tree data.
2019-05-09 Update BLAST UNITE filters to filter at taxon level one above for each tree.