BIRCH 3.90 Released

NEW  and Updated Software applications and features:
  • BioLegato version 1.1.2
    • PCD files now support include directive
    • About - Citation for BioLegato paper in BMC Bioinformatics
    • New Platform: macos-arm64
    • Export to CSV/TSV no longer encloses cells in double quotes
  • NEW - MacOS-ARM64 (phase I) - This is the first release to support macos-arm64, also known as Apple Silicon, M1, M2 or M3.
    • arm64 native binaries are now included for the following packages/programs
      • cd-hit
      • FASTA
      • FSAP
      • LAST
      • MAFFT
      • Phylip
      • pollux
      • primer3
      • Rcorrector
      • samtools
      • seqkit
      • Weighbor
      • XYLEM
    • All remaining x86_64 binaries currently run by hardware emulation by rosetta2
  • NCBI BLAST - updated to version 2.14.0+. Default for protein searches is now blastp-fast, blastx-fast and tblastx-fast. With this option, finding amino acid sequences with >=50% identity is much faster.
  • BLAST - substantial revision and updating of BLAST tutorial
  • FASTA - updated to version fasta36-36.3.8 (May 2023)
  • LAST - updated to version 1512
  • primer3 - updated to 2.4.0
  • Seqkit - updated to version 2.4.0
  • NEW - MaxAlign - removes sequences from a multiple alignment that result in excessive gaps
  • jellyfish updated to version 2.3.0 (linux only)
  • Quast updated to version 5.2.0
  • Rcorrector updated to version 1.0.6
  • SPAdes updated to version 3.15.4
  • samtools updated to version 1.179
  • salmon updated to version 1.10.1; transrate modified to use salmon 1.10.1

DELETED applications:
  • FSAP (obsolete) - intrest
  • XYLEM (obsolete) - findkey, xylem_identify, phyl2flat, flat2phyl
End of Life Platforms
RHEL 7 - Red Hat Enterprise Linux and related distributions will no longer be supported in future releases of BIRCH. Subsequent releases will be developed and tested on RHEL 8 or later.
Ubuntu 18 - Ubuntu LTS 18.0.4 LTS and related distributions will no longer be supported in future releases of BIRCH. Subsequent releases will be developed and tested on Ubuntu 20.0.4 LTS or later.

Python2 - BIRCH no longer requires python2. All python scripts now use python3.

Bug Fixes (See BIRCH Bugzilla at
  • getbirch.jar - For BIRCH installs over long distances, downloads would sometimes time out. This has been fixed by changing the download buffer size to 8192.
  • On some systems, Python scripts must be called by explicitly specifying 'python3', rather than 'python'. Although this can be fixed by installing python-is-python3, we are hardcoding 'python3' into python calls as an ongoing process. This release fixes some scripts, but others may still be present. 
  • For systems on which python 2 is not installed, the 'python' command will not be available. While installing python-is-python3 can fix that, we have eliminated most of these calls in the current release. The goal is that it will not be necessary to install python-is-python3 in a future release.
  • Weblogo - on some systems EPS output contained terminal messages, preventing files from being converted to PDF for viewing. Fixed.
  • Bugzilla #1211 - BioLegato table canvas exported fields in double quotes. This feature was originally for compatability with earlier versions of Excell, but caused problems when importing TSV files into BioLegato. Modern spreadsheets can read CSV and TSV files, so quoting is no longer used when exporting.
  • - is a wrapper script for running If an amino acid sequence ended with an 'X', would fail, complaining that the protein didn't match the DNA sequence. now changes 'X' to gap ('-') to avoid this problem.
December 31, 2023
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/ 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
  • 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
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
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