BIRCH 3.87 Released
  • BioLegato PCD files now support include directive
  • MAFFT - Updated to v 7.505
  • Minor documentation updates
 August 4, 2022
Version 3.86 (May 20, 2022)

NEW  and Updated Software applications and features:
  • In OSX, the desktop app to launch the BIRCH BioLegato application is in $BIRCH/admin/launchers/birch.app. Although BioLegato is a 64-bit Java application, the launcher was an old one generated when apps were 32-bit. Beginning with OSX Catalina, 32-bit apps will no longer run.  The BIRCH application was still able to launch from the command line. This app has been regenerated as a 64-bit launcher using Platypus on a High Sierra Mac.
  • Updated User Settings documentation with information on NCBI transition to 3rd party authentication.
  • NCBI database list has been updated to include the following databases newly available for FTP download: (env_nr, mito, pat_aa, refseq_select_prot)
  • FASTA has been updated to version 36.3.8i.
  • Jalview - updated to version 2.11.2.0.
  • FastQC - updated to version 0.11.9
  • Cytoscape - updated to version 3.9.0
  • Mesquite - updated to version 3.70.
  • trim_galore - updated to version 0.68
  • cutadapt - updated to version 3.7.
  • Trinity - updated to version 2.14.0
DELETED applications:
  • ArrayNorm - gives errors with most recent JavaVMs; package is no longer supported.

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)
May 20, 2022
Log4j2 vulnerability status
At present, it does not appear that any of the Java programs distributed with BIRCH presents vulnerabilities due to the log4j2 exploit. We have confidence in this assertion for several reasons:
  • Log4j2 applies only to Java applications
  • A scan of all Java applications, including source code and .jar files was done to identify potentially vulnerable applications.
  • Some older applications use versions of  log4j that are not susceptible to this exploit.
  • None of these applications acts as a web or peer-to-peer server
  • All BIRCH applications run with user permissions only. None uses admin permissions.
Out of an abundance of caution, further investigation into this potential problem are ongoing.This message will be updated accordingly.

We will take this opportunity to remind all BIRCH users that your best defenses against potential security threats are to
  •  run system updates on a routine basis
  •  back up your files offsite (eg. to the cloud or network-attached storage)
  • change your passwords frequently.
 December 21, 2021
BIRCH 3.85 Released
  • Web documentation reorganized for easier navigation and local customization at each BIRCH site.
Sept. 6, 2021
BIRCH 3.80 Released
  • improvements to BLAST search results
  • improvements and updates for multiple alignment and phylogeny
  • numerous updated software packages
  • extensive improvements to pre-processing and QC of sequencing reads
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July 5, 2021
BIRCH 3.70 Released
  • improvements and updates for multiple alignment and phylogeny
  • personalized user settings for BIRCH environment, including NCBI Entrez API keys
  • NCBI Entrez keyword searches now support Neighbor and LinkOut searches
July 22, 2020
BIRCH 3.60 Released
  • First time setup tutorial for MATE desktop
  • Python3 compliance
  • Updates to BLAST, FASTA database searches
April 26, 2020
BIRCH 3.50 Released June 20, 2019
BIRCH 3.40 Released
May 2, 2017
Installing and Searching Local BLAST Databases
May 19, 2016
BIRCH 3.20 Released May 19, 2016
BIRCH 3.15 Released
Jan. 6, 2016