History
2024-09-04 Add CIPRES BEAST tool.
2024-08-28 Add tool IQ-TREE on CIPRES.
2024-08-25 Debug underscore in TCS.
2024-08-20 Add Astral graphs tool to show gene tree conflict.
2024-07-16 Add archive file for popphy cnn.
2024-07-09 Start conversion of all scripts to Python3 for move to new server.
2024-07-09 Convert concatloci script to Python 3
2024-06-03 Add nexus option for fasta from list tool.
2024-05-16 Add viewerHeight to url of cytoscape popphy-cnn viewer to adjust view area.
2024-05-13 Add captch to quotes page.
2024-05-13 Add some example queries for query genbank for wheat.
2024-05-10 Add function to clean microsats submitted data.
2024-05-03 Add message if legend column is empty for splitstree.
2024-04-25 Update help block for Create Taxonomy tool.
2024-04-04 Update submit tool to submit microsats tree.
2024-04-01 Add option to query genbank to submit saved srcchk results and skip first step of tool.
2024-03-27 Catch entrez errors and retry in Create taxonomy.
2024-03-25 Add function to TCS to remove problematic chars.
2024-03-24 Catch entrez errors and retry in query genbank.
2024-03-24 Update query genbank for large query by splitting srcchk into parts.
2024-03-22 Update Cluster sequences tool to Python 3.
2024-03-22 TCS add function to rename haplotypes in reports.
2024-03-20 Update query genbank tool to allow result of 2 million.
2024-03-12 Add alt text option for scale bar in submit tree.
2024-03-06 Bug fix for submit tree.
2024-02-28 Add print btn for splitstree.
2024-02-27 Add Phylip to update names.
2024-02-09 PopPhy-CNN add options for L2Lambda, KernelWidth, KernelHeight, NumConvLayers.
2024-02-02 Add viewerheight for cytoscape PopPhy-CNN viewer.
2024-02-01 PopPhy-CNN add option for counts table format.
2024-01-30 Move blue hover box on guide tree.
2024-01-19 Add italicize legend for splitstree.
2024-01-17 Add clean data script for splitstree.
2024-01-16 Fix voucher with trailing spaces in data in TCS graph.
2024-01-11 Add option for extract short names with Retrieve names from tree or sequence file.
2024-01-08 Allow long names for sequence converter.
2024-01-08 Update multiple uploads for hmmer tool to avoid timeouts.
2024-01-07 Add nexus file to update names tool.
2023-12-19 Add NEXUS option to update names tool.
2023-12-18 Add some documentation for hmmer tool.
2023-12-07 Undo some changes to query_genbank tool that had been added to repurpose the tool.
2023-12-07 Update UNITE db to UNITE_public_25.07.2023.
2023-12-05 Add phipack to splitstree.
2023-11-28 Update hmmer tool for nuclear data for multiple loci.
2023-11-27 Add option for concat tool for hmmer files.
2023-11-20 Sequence converter add option to remove trailing q.
2023-11-17 Add option for Splitstree to create colors programatically and create blank metdata file with all custom columns or use custom metadata file.
2023-11-13 Add inputs for Splitstree to exclude list classes and list of strains to exclude.
2023-11-10 Update sequence converter tool to allow picking longest sequence if there are duplicates.
2023-11-09 Add Splitstree editor page to change marker size and labels display in SVG after the run is finished, and allow updated SVG to be downloaded.
2023-10-24 Create Genbank ids tool to add genus, species taxid to metadata file for use in viewing metabolites on TBAS
2023-10-20 Update some code in lulu library that caused a bug in tools.
2023-10-11 PopPhy-CNN add filter by kingdom.
2023-10-04 Update code in Splitstree to create colors.
2023-10-04 Bug fix for phmmer tool.
2023-10-06 Create new tool Rename FASTA headers to rename sequences by file name.
2023-10-02 Update to Merge Metadata tool.
2023-10-02 PopPhy-CNN add switchgrass example files.
2023-09-26 Add server for Celery to run PopPhy-CNN
2023-09-22 Create PopPhy-CNN tool
2023-09-21 Move PopPhy-CNN code into tools code so it can be copied for PopPhy-CNN tool.
2023-09-17 Splitstree rearrange graph, legend and scalebar to better fit with no overlaps.
2023-09-21 Add scalebar=yes option to Splitstree print command to print scalebar.
2023-09-14 Add to Splitstree print tree directly using Splitstee EXPORTGRAPHICS command line option.
2023-09-11 Add tool to show registered T-BAS on a map by country.
2023-08-22 Add tool to create tree from microsats data.
2023-08-15 Write script to update search for use in guide tree page.
2023-08-01 Add create tbas_taxids.txt file to gnps for use in display on T-BAS.
2023-07-21 Add navigation arrow to guide tree.
2023-07-07 Update mesquite block files for different grid sizes directly from Mesquite for possible errors using text replace originally.
2023-05-22 Add GNPS library search tool to get MS peaks from metabolite name.
2023-05-18 Add GNPS ontology tool to place MS results on ontology tree.
2023-05-15 Add option to Hypha tool to have custom colors for conflict boxes.
2023-05-14 Fix bug in print multipage PDF.
2023-02-28 Add Merge columns in T-BAS metadata file tool.
2023-01-30 Write Node js script to create legend for splitstree from metadata color columns, and update nexus file for splitstree program.
2023-01-18 Update query genbank tool to upload accessions file.
2023-01-17 Add color picker to Splitstree viewer.
2023-01-10 Add tool to retrieve submitted files by accession id.
2022-12-21 Add option for splitstree to skip print graph due to long running calculation for distance matrix.
2022-11-22 Add script for citations page to transform DOI in citation to a link to the article.
2022-11-18 Update scripts for new server names.
2022-10-03 Add font options for Splitstree viewer.
2022-09-19 Add Captcha to Contact Us page to stop bots.
2022-09-06 Add new tool to retrieve treebase files from local database.
2022-08-11 Add new tool to display splitstree graph with D3.
2022-07-11 Create new tool guide_tree_edit to easily add submitted trees to TBAS guide tree.
2022-06-29 Update TBAS guide tree to automatically show legends.
2022-06-28 Add splitstree option to tcs_graph tool.
2022-06-24 Add option to use a GML file as input to tcs_graph tool.
2022-06-10 Update Mesquite template.
2022-06-06 Add LULU, create neighbor-joining tree, rarefaction, and filter functions to phyloseq tool.
2022-06-05 Add code from Matthew Willman for normalized barplots in phyloseq tool.
2022-05-20 Add new tool Phyloseq that uses as input an R object file created by dada2 and remove phyloseq from dada2 scripts.
2022-04-19 Add dada2 script for non-overlapping with primers already removed.
2022-03-18 Update SILVA database to v138
2022-03-18 Add package version info to dada2 emails.
2022-03-17 Update gmail account to use authenticated mailer.
2022-01-11 Change mailer program to send from tbasncsu@gmail.com
2021-12-14 Remove save stdout for imgc tool run locally.
2021-12-03 Add summary report for Create protein or DNA locus files using phmmer or nhmmer output tool.
2021-11-18 Added 2 tools to monitor jobs submitted to CIPRES.
2021-10-26 Add IMgc tool that runs on CIPRES
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.cifr.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.