Phylogenomic Tools

List of new tools, features, bug fixes, and issues in DeCIFR tools

History

  • 2020-08-06 Update main Flask page that serves web pages from Python 2 to Python 3.

  • 2020-08-02 Add new tool to update names in a newick tree file or sequence file with replacements from csv file.

  • 2020-07-24 Add option to Get names from a tree or sequence file to create a csv with best guess for scientific names.

  • 2020-07-16 Add tool to get names from tree or sequence file.

  • 2020-07-11 Change landing page for decifr.hpc.ncsu.edu and also menus for all the DeCIFR tools.

  • 2020-06-26 Add option to BLAST tool to use NCBI REST interface.

  • 2020-06-02 Bug fix. Fix reading NEXUS files with quoted trailing space not removed.

  • 2020-06-02 Update set results tool to allow more than 2 files and to read sequence names in addition to file lists.

  • 2020-05-29 Add directory locus_csvs for dada2 for ASV summary files for all cases.

  • 2020-05-19 Add button for SNAP Workbench on Galaxy.

  • 2020-04-22 Fix NCBI blast to place correct rank in taxonomy report columns.

  • 2020-04-09 Add to BLAST tool rbclX database for Peltigera.

  • 2020-04-06 Create Extend alignment tool to append or prepend a sequence that has overlap regions without duplicating sections.

  • 2020-03-30 Add NCBI database to BLAST tool.

  • 2020-03-26 Add IMgc and script to IMa3 tool to create IMa3 formatted input file from fasta files.

  • 2020-02-20 Add create unrooted tree to Collapse nodes with low bootstrap support.

  • 2020-02-12 Add Isolation-with-Migration (IMa3) tool with IMfig graphics output script to create figures.

  • 2020-01-14 Move the calculations for the ITSx tool to a second server and run the jobs using the Python Celery library jobs queue to limit the number of jobs run at once to 4.

  • 2020-01-12 Add calculations to cluster tool to create fasta files for locus2,3,4... that correspond to the OTUs created for locus1 and save in a directory with the centroid fasta file for locus1.

  • 2020-01-10 Add options to ITSx tool to select E-value and database. Also set to run on 2 CPU.

  • 2020-01-06 Add ability to view sequences to telescope viewer.

  • 2019-12-18 Add tool to download mep archives from permanent storage.

  • 2019-11-22 Update Create haplotype table to use vsearch or QIIME.

  • 2019-11-15 Add tool to download FASTA and metadata for query of GenBank.

  • 2019-11-06 Update telescope viewer to collapse by depth instead of by attibutes. Update to work for rectangular layout. Allow click to expand without selecting from popup menu.

  • 2019-10-13 Add logout/login button to navigation bar. Add contact us button.

  • 2019-06-26 Add tool to concatenate several tree files into one hypha file and display tree with grid boxes.

  • 2019-05-31 Send email to user when submitted tree is available.