Phylogenomic Tools

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

History

  • 2021-01-14 Add new tool - Create protein locus files from annotations using phmmer output

  • 2021-01-13 Fix bug showing alignments with TCS tool with missing partition table and too long alignments causing tool to fail.

  • 2020-11-17 Move IMgc perl script to run on celery server and add password protection to redis server to prevent abnormal run termination.

  • 2020-11-13 Add additional step to R script for dada2 to remove primers.

  • 2020-11-13 Update html on DADA2 page to change drop down box to radio buttons and reset buttons for drop boxes

  • 2020-10-25 Add FASTA from list tool to extract sequences in FASTA file by using a list. Add Extract chromosome FASTA tool to create several chromosome FASTA files from a single file and a map file.

  • 2020-09-29 Add tool to convert sequences from FASTA, PHYLIP, OR NEXUS to one another. Also include report for each file for sites variable and constant and an option to convert ambiguous characters to N.

  • 2020-08-19 Add option to structure plots tool to edit the colors in the histograms.

  • 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.