Phylogenomic Tools

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

History

  • 2021-10-21 Convert 4 scripts that run on remote server with Celery to Python 3. Add Flower-Celery monitoring tool to remote server to monitor jobs.

  • 2021-09-16 Add template for 3x3 hypha trees.

  • 2021-09-16 Add option to set cluster value in BLAST tool. Remove srcchk step from NCBIWWW BLAST and use instead species name in result.

  • 2021-08-30 Add function that can remove hidden control characters from csv files.

  • 2021-08-12 Fix 2 bugs in BLAST tool. One was OTU duplicates not being added to fasta files, and the other was running wrong BLAST program when extra taxon fasta file was selected.

  • 2021-08-06 Update UNITE database to version 8.3, release date 2021-05-10

  • 2021-07-08 Create tool to return CIPRES XML from CIPRES run URL.

  • 2021-07-08 Update hypha to better place bootstrap number for trees with different numbers of conflict blocks.

  • 2021-07-01 Update de novo tree tool with RAXMLNG and option to run faster best-scoring ML tree or slower All-In-One analysis to get bootstrap supports.

  • 2021-06-14 Add error handler to show error in FLASK code instead of a 500 Internal Server Error page.

  • 2021-06-15 Update HMMER tool to extract results from nhmmer.

  • 2021-06-10 Add multimodel option to RAxML tool.

  • 2021-06-07 Convert TCS tool to use Python 3.

  • 2021-04-19 Fix use previous run option on DADA2 tool that allows user to not upload the same data for a new run.

  • 2021-03-12 Update the Create FASTA locus files from genome annotations tool to convert metagenome file.

  • 2021-03-10 Add new tool to view tbas results database by specimen name. Also read data from tables in the GoLife database.

  • 2021-02-23 Create tool to get ncbi taxomomy from scientific names.

  • 2021-02-17 Add view structure to rectangular view in structure tool.

  • 2021-02-05 Add option to BLAST proteins for the fungal taxonomy tool.

  • 2021-01-25 Add option to ladderize tree to Hypha tool

  • 2021-01-24 Add allow multiple files input to Newick to Nexus format tool

  • 2021-01-15 Create new tool - Database Viewer to display T-BAS results by run id

  • 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.