BIRCH Version 4.0D

NEW:

BIRCH: A user-oriented, locally-customizable, bioinformatics system
Brian Fristensky
BMC Bioinformatics 2007, 8:54 (9 February 2007)
[Abstract] [ PDF]

BIRCH is

a comprehensive desktop bioinformatics system which comes with many of the commonly-used bioinformatics programs pre-installed
a framework of tools, files, and documentation for organizing and managing a bioinformatics core facility
an expandable system that allows you to merge 3rd party programs and documentation seamlessly into the standard BIRCH distribution

DOWNLOAD BIRCH NOW

New in the current release:

Current Development Version 4.0D (June 17, 2024)

NEW and Updated Software applications and features:

features - To eliminate the dependency for installation of tcsh, features has been completely re-written in Python as features.py.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Fixed: For output to a fasta file, getob failed to write a line break after the name line.
Fixed: When reading a nucleic acid file without a name line, ribosome skipped the first nucleotide, throwing off the open reading frame.
Fixed: splitdb would terminate an index file with non-printing control characters.

Current Stable Version 3.90 (December 31, 2023)

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 Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

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.
pal2nal.py - pal2nal.py is a wrapper script for running pal2nal.pl. If an amino acid sequence ended with an 'X', pal2nal.pl would fail, complaining that the protein didn't match the DNA sequence. pal2nal.py now changes 'X' to gap ('-') to avoid this problem.

Version 3.87 (August 4, 2022)

NEW and Updated Software applications and features:

BioLegato 1.1.0

BioLegato PCD include directive - BioLegato now has a preprocessor, similar to the C include directive, that substitutes PCD code from an external file, prior to parsing. Thus, any BioLegato blmenu file can include PCD from a file. This is particularly useful for blmenus that display lists, such as lists of locally-installed databases. The include directive adds greater flexibility to how BioLegato menus can be constructed.

BLAST databases - BLAST databases are no longer available from EMBL-EBI. This site has been removed from blastdbkit.py. Databases can still be downloaded from NCBI and DDBJ.
MAFFT - Updated to v 7.505, which fixes an important memory allocation bug.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

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)

log4j2 - 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.

Version 3.85 (September 6, 2021)

NEW and Updated Software applications and features:

This release introduces a new BIRCH home page that should be easier to navigate and customize, as well as being more aesthetically appealing than the prior home page. It is enough of an improvement that it's worth upgrading from 3.80.

Rather than having all main links displayed on the home page, links have been organized into a navigation bar with dropdown menus. This still allows the user to find what they want almost instantly, without the screen clutter of the previous version of the web site.

Local pages, such as instructions for connecting to a BIRCH server, or first time setup, are can be seamlessly integrated into the nav bar menus. This helps the new user see how to do things on their site.

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Version 3.80 (July 5, 2021)

NEW and Updated Software applications and features:

samtools upgraded to version 1.12
SeqKit upgraded to version v0.15.0
LAST - upgraded to version 1219 9
Bandage - (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates interactive visualisations of assembly graphs.
bldna

Added launcher to open NEBcutter website to draw restriction maps.

blpalign

NEW: pal2nal.py by Mikita Suyama - aligns DNA to a protein alignment.

BLAST

Added option to Database menus in bldna and blprotein to display information on locally-installed databases using spreadsheet.
Added option to BLAST menus to search user-created BLAST databases
bldna,blprotein - added makeblastdb to create a blast-formatted database from a set of sequences.
BlastViewer - Updated to version 5.5.1.

Phylogeny:

New: Gblocks from Jose Castresana - removes poor quality or gappy regions from multiple sequence alignments prior to phylogenetic analysis.
All phylogeny programs run through blnalign and blpalign now send output to the Archaeopteryx tree editor. If sequence names are sequence accession numbers from NCBI, Archaeopteryx can retrieve sequence information such as name, taxonomy id etc. for addition to the tree.
blnalign, blpalign: dnapars and protpars can now accept user trees generated through bootstrapping.
bltree - New option to run confadd to add bootstrap confidence numbers to trees. Creates a phyloXML file which can be viewed in Archaeopteryx.
Updated phylogeny tutorials to illustrate new features

blreads

NEW: adaptercheck.py - searches fastq files for potential read-through contaminants in sequencing reads
NEW: fixfq.py - split a fastq file into two files, respectively containing valid reads and bad reads
NEW: fastalen.py - split sequences from a fasta file into 1 or more files depending on sequence length
New features for creating subsets from read files for reads that match a database. Eg. to remove reads from contaminating species

magicblast - create list of reads matching a BLAST database
seqkit grep - extract reads which match or mismatch reads found by magicblast

NEW: seqkit fq2fa - converts fastq files to fasta files
NEW: seqkit convert - converts from one Illumina fastq format to another

bl_rename.py can do bulk renames of files in the current directory. Added options to remove blanks, change blanks to other characters, or change to Camel Case.
Trimmomatic - added option to read a file of custom adapters to trim
hisat2 map - Added feature to run samtools stats to generate statistics for each .bam file created.
The Genome and Transcriptome menus have been reorganized to better reflect object-oriented style.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

DNAML, PROML - couldn't run with user-specified tree.
bldna, blprotein, blnalign, blpalign - some temporary files were not deleted
blreads - Abyss failed to run if primary read set selected in blreads was single-end reads
On some multiuser systems, users other than the BIRCH administrator would not have permissions needed for local configuration files. Permissions have been fixed.

Version 3.71 (July 29, 2020) - Feature upgrade to 3.70

NEW and Updated Software applications and features:

BLAST search improvements:

Results of BLAST searches now pop up in BlastViewer, in addition to the web browser report and BioLegato spreadsheet. BlastViewer gives the user a comprehensive environment for evaluating BLAST results.
For computers running a mail server, email notifications can be sent when long-running BLAST jobs are completed.

Added BIRCH launcher to Activities menu in Linux/GNOME3 shell.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Version 3.70 (July 22, 2020)

NEW and Updated Software applications and features:

Jalview updated to version 2.11.1.0
ClustalOmega v 1.2.4 (MacOSX: v 1.2.3)
MAAFT has been updated to v 7.470.
Archaeopteryx updated to v 0.9928. Archaeopteryx is now the default phylogenetic tree editor for BIRCH.
cd-hit v 4.8.1 - cluster and remove redundancy from nucleic acid and amino acid files
uniqid.py - Replaces names in fasta files with unique numeric codes. The Phylip programs truncate sequence names longer than 10 characters. blnalign and blpalign run uniqid.py -encode to replace sequence names with unique numerical codes of 9 characters in length. A separate TSV file is also created that maps the original names to the encoded names. These are used as input for Phylip programs to restore the original names to output files.
birch - BIRCH now lets the user set preferences for helper applications, as well as things like setting the command prompt, the email address for notifications of completion of long-running jobs, and the NCBI API key. Settings can be changed in the Edit menu of the birch application.
NCBI Eutils:

Support for NCBI Eutil API keys - Users planning to make large numbers of requests to NCBI Entrez databases (eg. keyword searches for sequences), should get an Entrez API Key from NCBI. Your API Key can then be set in birch --> Edit --> Settings, along with your email address. ncbiquery.py, seqfetch.py and taxfetch.py now support these keys.
replaced the older Perl version of xtract with the latest C version of xtract

DELETED applications:

TCOFFEE
ATV tree editor
fastDNAml

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

fasta tabular output, using the -m F8C option, would fail for some databases, resulting in a failure of output to appear in blnfetch or blpfetch. The SubjectID field for most databases takes the form "gi|667489388|ref|NC_019843.3| ". However, some databases, such as Betacoronavirus, have only an accession number for this field eg. "MN541280.1". This latter form would cause blfastaout.py to crash. blfastaout.py now correctly handles both forms for the SubjectID field. Also, blfastaout.py failed to retrieve information on hits to the human_genome and mouse_genome databases, because the files for those genomes prefixes GCF_000001405.38_top_level and GCF_000001635.26_top_level, respectively. blfastaout.py now correctly retrieves information from those files.
blncbi/ncbiquery.py - Fixed calls to the Eutils elink function, so that searching for entries linked to queries now works.

Version 3.60 (April 24, 2020)

NEW and Updated Software applications and features:

Python3 compliance - The install process and most scripts should now be completely Python3-compliant. BIRCH now requires Python3.
First time setup tutorial for MATE desktop
NCBI BLAST+

updated to version 2.10.0
blastdbkit.py now installs and manages local BLAST v5 databases.
bldna, blprotein - updated to work with BLAST databases as reorganized in v5.
updated BLAST and FASTA tutorials for v5 databases

FASTA

updated to v36.3.8h
output to HTML and blnfetch, blpfetch

blnfetch, blpfetch can now export to a spreadsheet eg. LibreOffice Calc
WebLogo updated to v3.7. (Linux x86_64 only. Weblogo 3.7 requires Scipy libraries, which fail to compile on OSX. Therefore, OSX still uses the Python-only Weblogo 3.4.)
OSX desktop launcher - Replaced older 32-bit launcher with 64-bit launcher

DELETED applications:

Deleted old libraries in lib-linux-x86_64: jellyfish, fc4libs, gde.fonts, openwin. These were needed by applications that are no longer included in BIRCH.
tacg

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Version 3.50 (June 20, 2019)

NEW and Updated Software applications and features:

This release represents a massive addition to the BIRCH system, with complete sets of tools for genome and transcriptome assembly and gene expression data. Most of these capabilities are unified in a new BioLegato interface called blreads. Because most genome and transcriptome tasks work with numerous files, blreads presents the files as a spreadsheet (akin to a file manager) in which files can be selected as input for a wide variety of programs. Because these tasks are time-consuming, notification of completion by email is supported.

Sequencing read pre-processing and quality control

SeqKit -tasks and statistics on reads
trim_galore/cutadapt - adapter trimming
Trimmomatic - adaptor trimming
Pollux - DNA read correction
Rcorrector - RNA read correction
fastq_pair - eliminate non-paired reads from paired-end files

Genome assembly and annotation

ABySS - Genome assembly
SOAPdenovo2 - Genome assembly (Linux only)
SPAdes 3.13.0 - Genome assembly
Quast - Genome assembly quality report
GFF Utilities (http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare)
NCBI tbl2asn updated to version 25.6.

Transcriptome assembly and gene expression

rnaspades - RNA transcript assembly
SOAPdenovo-Trans - RNA transcript assembly (Linux only)
Trinity - RNA transcript assembly (Linux only)
transrate-1.0.3
Hisat2 v 2.1.0 - map RNA reads to genome (supersedes TopHat)
stringtie (supersedes cufflinks)
ballgown (supersesdes cuffdiff) (R pkg)

BioLegato v1.0.4

overwrite implemented for Table canvas
Value fields for Text and Number variables allow environment variable substitution.

blnfetch, blpfetch can now retrieve sequences from local BLAST databases or FASTA files

Utilities

jellyfish
salmon
samtools v1.7 (needs documentation, testing)
makelinks.sh - creates symbolic in current directory to files in a source directory
pigz - parallel implementation of gzip/gunzip. Speeds up handling of compressed read files

Other

NCBI sequin - will be phased out by NCBI. Not updated

Artemis 17.0.1

REBASE has been updated to release Feb. 26, 2019

DELETED applications:

none

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Bugzilla #1220 - blnalign, blpalign : Phylip programs fail for some proteins with YF. Fixes a very old bug that would rarely occur.
Bugzilla #1218 - overwrite was not implemented for Table cavas.
On Mac OSX, the default for BioLegato interfaces using the table canvas (ie. blnbci, blnfetch, blpfetch, blmarker, bltable) had no borders around cells, which detracted from readability.

Version 3.40 (May 2,2017)

NEW and Updated Software applications and features:

Comparative Genomics

Bltable - simple spreadsheet version of BioLegato for generic spreadsheet data.
Tutorial: Finding and retrieving sequences from NCBI
Tutorial: in-silico PCR of genes using NCBI Primer-BLAST
bldna,blprotein - View sequence now defaults to GenBank format.
blncbi - PROTFETCH now defaults to retrieve sequences to blprotein, rather than text editor.
blastdbkit.py - better recovery when downloading a BLAST database fails.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Bugzilla #1213 - human and mouse genomic_transcript not deleted by birchadmin- These GenBank divisions were not deleted by blastdbkit.py --delete. Another bug was fixed which prevented email notifications from being sent when blastdbkit.py completed.
Bugzilla #1214 - chooseviewer.py fails to open html files on MacOSX
Bugzilla #1215 - bldna,blprotein - When launching DXHOM, PXHOM, TESTCODE, NUMSEQ with no data selected, programs would run in an infinite loop.
Bugzilla #1216 - PXHOM can't work with lowercase amino acids
Bugzilla #1217 - MacOSX - directory chooser fails to popup

Version 3.30 (November 21,2016)

NEW and Updated Software applications and features:

BLAST+

upgraded to version 2.5.0
hits now viewable in HTML, and in a detailed hit summary including in tabular form in blnfetch and blpfetch. The tabular output vastly improves the user's ability to sift through large numbers of hits based on many sorts of output criteria.

BioPython has been upgraded to v 1.68. In particular, this release of BioPython supports the NCBI shift to using HTTPS for web services, rather than HTTP.
FASTQC - Graphical Quality Control Tool for assessing quality of NGS sequencing reads.
Compliance with the phase out of GI numbers from NCBI databases:

blncbi now retrieves document summaries with Accession numbers, not GI numbers
Output from BLAST and FASTA now parses only Accession numbers into separate lists. GI numbers are ignored. These programs should still be backward compatible with NCBI old database files that include GI numbers.
delgi.py - Remove GI numbers from GenBank flatfiles, in compliance with the NCBI phase out of GI numbers. The purpose of this script is to create GenBank flatfiles conforming to the new format, as test files for ensuring that software works with these format changes.

BioLegato 1.0.3

BioLegato can now run any process in the background. This makes it possible to launch long-running jobs, close BioLegato, logout, and still have the job running until complete. In PCD .blmenus files, the shell command should take the form:
shell "(command)&"
Examples can be found in .blmenu files. Tasks such as database searches and database file installation have been updated to take advantage of this feature.

dotter - DNA and protein dotplots. Supports GFF files for genome features. (Linux only).
blsort.py - now supports floating point numbers, in addition to integers and strings.
birchprops - New tool for managing properties of your BIRCH installation. The current version has only one option, to set URLs that will make the documentation for your local BIRCH documentation readable on the Web. This will only work if your machine is set up as a web server.
bldna, blprotein - Added Fasta to list of formats saved using Save Selection As
NCBI Sequin updated to v15.10

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Bugzilla #1212 - Getbirch hangs when decompressing archive files during an install/update.
BioLegato - output to GenBank file inserts an extra blank line before ORIGIN line.
Bugzilla #1209 - Local URLs for documentation not preserved in update.

version 3.20 (May 18,2016)

NEW and Updated Software applications and features:

blastdbkit is a Python script that makes it easy to install and maintain your own copies of NCBI BLAST databases, so that you can search databases using either the BLAST or FASTA programs.
Features:

can be run at the command line, or in a point and click interface through birchadmin
functions: Add, Update, Delete
generates spreadsheets showing disk usage of local databases, and estimates of disk space needed for files databases to be downloaded
email notification when downloads and installs are complete
for quicker downloads, choose the FTP mirror closest to you
all local databases can be searched using either BLAST or FASTA through the BioLegato interface or the command line

Standalone BLAST+ updated to version 2.3.0.
blncbi - New search term to limit searches to a specific molecule type eg. genomic, mRNA, guide RNA, lncRNA etc.
BIRCH News - This page contains information on the latest features, brief How-To's, short articles on useful BIRCH features, and announcements of new releases. It is linked in the Documentation section on the BIRCH home page.

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

blncbi - Import from CSV: incorrectly used comma, rather than TAB, as field separator for TSV files.

version 3.15 (January 6,2016)

NEW and Updated Software applications and features:

Jalview has been upgraded to version 2.9.0b2.
seqfetch.py, blnfetch, blpfetch - now can retrieve sequences from NCBI using ACCESSION numbers or GI numbers. The previous version could only retrieve by GI number. However, NCBI is in the process of phasing out GI numbers, so future development will focus on retrieval by ACCESSION.
bldna,blprotein, blnalign,blpalign - view sequences and annotations in a text editor, using variety of formats. This is especially useful for pasting sequences into web applications.
MAAFT- Multiple sequence alignment by Fast Fourier Transformations.

DELETED applications/features:

The environment variables BLBIRCH_HELP_DIR, BLDNA_HELP_DIR etc. are obsolete, and have been removed from admin/profile.source and admin/cshrc.source.

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

version 3.10 (July 20,2015)

NEW and Updated Software applications:

Artemis - The Artemis sequence viewer/annotator has been updated to version 16.0.0. It is now possible to retrieve sequences from NCBI directly to Artemis, and to export sequences from bldna to Artemis.
First time setup documentation has been added for the MacOSX desktop.
Automated customization for settings and Helper Applications. This release introduces a Preferences menu to birchadmin, that lets the user choose Helper Applications for viewing output in different file formats (eg. HTML, PDF, text, graphics). chooseviewer.py determines the type of file and launches the appropriate application.
The BIRCH update/install wizard, getbirch, can now be launched from birchadmin.
Substantial updating of documentation for BIRCH system administration.
Some BIRCH environment variables that goven how BIRCH behaves can be set in the BIRCH Administration Tool (birchadmin). These variables are no longer set in $BIRCH/local/admin. If you are upgrading from BIRCH 3.0 or earlier, they can be deleted from local.profile.source and local.cshrc.source.
These include:
- all GDE variables (eg. GDE_TEXTEDIT, GDE_PDF_VIEWER etc.)
- BIRCH_TMP
- BIRCH_LOGGING
- BIRCHJAVACMD
- BIRCH_NETSCAPE
- BROWSER_OPENURL
- lines setting the shell prompt

DELETED applications:

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Note: Weblogo requires the Python numpy library, which is not distributed with BIRCH. Instructions for installing numpy can be found here.
Bugzilla #1202 - update_local.py fails to copy files to $BIRCH/local

version 3.00 (May 2,2015)

NEW and Updated Software applications:

New BioLegato interfaces for NCBI Entrez queries and retrieval
The middleware for these BioLegato interfaces consists of two Python scripts, ncbiquery.py and seqfetch.py that can also be used at the command line. These scripts utilize the BioPython Bio::Entrez API.

blncbi: lets users construct Entrez queries to NCBI and returns results in spreadsheet form, for subsequent retrieval.
blnfetch: retreives nucleotide sequences from remote BLAST or local FASTA searches.
blpfetch: retrieves amino acid sequences from remote BLAST or local FASTA searches.

BioPython 1.65 is now distributed as part of BIRCH, in the $BIRCH/python directory.
WebLogo 3.4 - Create sequence logos from multiple DNA or protein alignments
BioLegato 1.0.2 -
- Export Foreign Format (bldna,blprotein,blnalign,blpalign) - Now has an option to export to a text editor. This is very useful if you want to copy sequences from BioLegato to paste into a web form. All formats supported by READSEQ are available.
- blnfetch, blpfetch - new BioLegato interfaces that use the NCBI Entrez utilities to retrieve DNA, RNA or amino acid sequences from NCBI.
- bldna and blprotein will send GI or ACCESSION numbers from BLAST hits directly to blnfetch or blpfetch for easy retrieval of sequences.
- bldna - GFETCH - retrieve sequences from NCBI using GI or ACCESSION numbers.
- PCD has a new type called "textarea" that creates a text box in a menu. Any text can be pasted into the text box, such as lists of GID numbers or sequences.
- pcdedit - graphical editor for PCD menus. Still considered an experimental program.
- BioLego sequence canvas can split horizontally, allowing one to scroll horizontally through two parts of a DNA or protein alignment simultaneously.
As a milestone toward making BIRCH completely platform independent the install scripts have been entirely re-written in Python. The shell scripts in install-birch are no longer distributed, and are replaced by Python scripts in install-scripts.
NCBI Sequin - Updated to Version 13.70 on linux-x86_64 and MacOSX. NCBI appears to no longer be supporting Solaris or 32-bit Linux. Consequently, the solaris-sparc, solaris-amd64 and linux-intel binaries have been updated to Version 13.05, the latest version for these platforms.

DELETED applications:

Bluejay
Seahawk
generic_ncbi_data_fetcher.pl

Bug Fixes (See BIRCH Bugzilla at Bioinformatics.org: http://www.bioinformatics.org/bugs/?group_id=543)

Bugzilla #1141 - In some installs, the code from htmldoc.py that generated web pages that indexed programs would fail, resulting in blank web pages.
Linux: added new libXrender.so and libXfixes.so libraries to bin-linux-x86_64 for compatabilty of xace with new linux releases.
Bugzilla #1182 - BIRCH installer now compares date of currently installed version to prevent installing an older version over a newer version.
Bugzilla #1183 - Edit --> copy should use FASTA format. Solved by adding Export Foreign Format to send output to a text editor.
Bugzilla #1184 - GetBirch failed to run update-local.sh. The latter has been replaced with a Python script, update-local.py, which is run by GetBirch.
Bugzilla #1185 -Need more robust way to recover if BIRCH download fails. Several improvements so that BIRCH only needs a good $BIRCH/local directory for an update to be successful.
Bugzilla #1186 - Does UNINSTALL-birch.py need to run nobirch.py?
Bugzilla #1188 - SaveAs ignores selection and saves all sequences.
Bugzilla # 1190 - BioLegato failed to read GenBank entries containing the CONTIG keyword. Fixed, so that now BioLegato will create 0-length sequence when reading CONTIG entries. A more sophisticated fix would be to retrieve the complete CONTIG from NCBI, but because these are often in the hundreds of millions of nucleotides, for now we won't go that route.
Bugzilla #1197 - temp files deleted before chooseviewer.py can open them
Bugzilla #1198 - BioLegato can't delete characters unless sequence is in a group
Bugzilla #1199 - Cut and paste in a multiple alignment deletes gaps

version 2.96 (May 21, 2013)

NEW and Updated Software applications:

Reorganization of multiple sequence alignment tasks - Tasks for displaying and working with multiple sequence alignments have been moved from bldna and blprotein into two new BioLegato interfaces: blnalign for aligned DNA or RNA sequences, and blpalign for aligned protein sequences. For example, if you run TCOFFEE from blprotein to produce a multiple alignment, the output will be sent to blpalign. blpalign can be used to run tasks that only make sense with aligned sequences, such as phylogenetic analysis or alignment display. By making BioLegato adhere more strictly to object-oriented organization, it becomes more difficult to accidentally run tasks such as phylogeny using unaligned sequences as input.

As part of this reorganization, mrtrans can now only be run from blpalign. This makes sense, because it forces the user to already have a protein alignment before trying to run mrtrans.
Local BIRCH web site now displays current release number and timestamp.
BioLegato.0.7.9

BioLegato can now Copy and Paste using the system clipboard. This makes it possible to paste seqences from documents, emails etc. into BioLegato, and to paste sequences from BioLegato into web programs.

numerous bug fixes and performance enhancements including:
ability to set the text in the BioLegato window header bar
ability to specify order of items in a PCD menu
fixes to table canvas selection
fixes to PCD's platform specificity options
import column headers from file in table canvas
better ability to skip improperly constructed PCD menus

the BIRCH Launcher and birchadmin tool now have a launcher for Release Notes.

The BLAST+ programs from NCBI replace blastcl3 (netblast). New menus in bldna and blprotein expand the number of search parameters that can be set.
SHUFFLE - The option to manually set a random seed when running SHUFFLE has been eliminated from bldna and blprotein. Instead, the script that runs SHUFFLE generates a random seed. Previously if the user didn't set a random seed each time, the same random sequence was generated each time the program was run. There is no obvious advantage to setting a random seed manually, so it is best to just do it automatically to be sure it gets done.
Calculation of protein statistics such as molecular weight, pI and amino acid frequencies is done by a new program gstat.py, launched from blprotein.
Archaeopteryx is a fully-featured program for drawing phylogenetic trees, and overlaying other sorts or data onto trees. Archaeopteryx is the successor to ATV. In future releases, Archaeopteryx will replace ATV. Currently, it can be launched from bltree.

DELETED applications:

NCBI blastcl3 (netblast)
prostat and dbstat have been replaced by gstat.py (see above)

Bug Fixes

On a multi-user BIRCH system on MacOSX, if a user who is not the owner of BIRCH clicks on the BIRCH launcher icon, they get a permission denied error. (Bugzilla #1178)
A bug has been fixed in BACHREST, which prevented setting the minimum and maximum length of restriction sequences to search for. (Bugzilla #1174)

version 2.95 (September 24, 2012)

NEW and Updated Software applications:

Cytoscape v2.8.3 - Visualize biochemical pathways
NCBI BLAST+ v2.2.26 - blastp,blastn, blastx, tblastn, tblastx, blast_formatter.

DELETED applications:

TM4 MIDAS

BIRCH

In this version of BIRCH, all BioLegato menus have been translated into a new menu language called BioPCD. BioPCD expands on the functionality of .GDEmenus, and this functionality will expand in future versions. The old .GDE menus are no longer used. During an upgrade from previous versions of BIRCH, your old GDE menus in $BIRCH/local will be translated into BioPCD. All future development of local menus should be done using BioPCD.
The following environment variables were previously deprecated,and are now removed from $BIRCH/admin/cshrc.source and $BIRCH/admin/profile.source : $DATA, $data, $DB, $db. In particular, it was discovered that then $DATA was set, it would prevent LibreOffice v3.3 and later from launching. See bugzilla.redhat.com Bug #834800.
NEW: birchadmin - This BioLegato tool performs administrative tasks for the BIRCH system. It can be launched from the BIRCH launcher. New functions include: htmldoc.py, customdoc.py, lbirchdb. birchadmin can only be run when logged in as the BIRCH administrator.
BIRCH launcher: The DNA, protein, and Multiple alignment menus have been merged into a single menu called "Sequence".
When launching bldna, blprotein, blmarker or bltree from the BIRCH launcher, the user is prompted to choose a working folder.
BioLegato - tool tips and icons have been added to most menus in BioLegato
BioLegato - it is now possible to set the title to appear at the top of a BioLegato window.

version 2.9

fixed a bug in the script that runs mrtrans that prevented mrtrans from running on some OSX systems.
ribosome - In the previous release, the new version of ribosome was omitted from OSX and linux-intel binaries. The new version is now available on all platforms. (Bugzilla# 1167)
The Phylip package has been upgraded to version 3.69.
The BIRCH launcher now prompts for a working folder when started at the command line. This results in all programs launched from the launcher opening in the working directory, rather than the home directory.
acedb - on some Mac and Linux systems, acedb failed to launch because of missing libraries. These libraries have been added to the current release. (Bugzilla #1156)
bioLegato.0.7.7a:

fixed a bug in bioLegatthat prevented canvas from appearing
fixed a bug that prevented sliders in menus from having negative values (Bugzilla# 1160)
fixed a bug that prevented bioLegatfrom reading some legacy .gde files. If the sequence contained newline characters, those were included in the sequence (Bugzilla# 1161)
fixed a bug in which pseudo-GenBank files generated by GDE were not read
fixed a bug which prevented the Documentation menu from being used. (Bugzilla# 1160)

version 2.8.6

fixed critical bug in bioLegato 0.7.7 which prevented menus from displaying properly

version 2.8.5

bioLegato has been upgraded to v0.7.7. This version introduces
the new table canvas, which is used by blmarker.
ribosome: new options for formating translated amino acid sequences
The following programs have been removed do to obsolescence:
- GDE (gde, mgde, tgde) - superseded by bioLegato programs bldna, blprotein, blmarker, bltree
- clustalw, clustalx - these are superseded by TCOFFEE
- Translate - superseded by ribosome

version 2.8

Getbirch - Getbirch is an automated install updater and installer, that supersedes these functions in birchconfig. Birchconfig is still used for adding local custom documentation and for uninstalling.
bioLegato has been reorganized into several new interfaces:
- birch - launcher for all GUI programs in BIRCH
- bldna - DNA/RNA sequence tasks
- blprotein - protein tasks
- blmarker - molecular markers
- bltree - phylogenetic trees
When upgrading from BIRCH 2.7 and earlier, local GDE menus items will be copied to corresponding directories in local/dat. It is important to do a manual check to see if menus have been added to the appropriate bioLegato interface.
Visualization of data in bioLegato now includes a variety of character color themes for proteins, nucleic acids, markers and phylogenetic trees.
During a new installation, birchhome.sh failed to change the userid of the BIRCH administrator in passwd.wrm, both for birchdb and lbirchdb. This prevented creation of a local birch database, meaning that documentation for locally-installed programs wouldn't appear in the database. This has been fixed.
A major reorganization of Python scripts has been done. This addresses future compatibility with Python 3, as well as creating sets of reusable classes that will simplify future development.
A number of the bioLegato scripts failed to clean up temporary files after execution was completed. These have been fixed.
The Phylip programs drawgram and drawtree require the libXaw.so.7 library, which is not found in some Linux distributions. This library has been added.
PostScript files on MacOSX. The utility script PStoPDFviewer.sh automatically runs ps2pdf to convert PostScript files to PDF. However, ps2pdf appears not to be part of the standard OSX install. PStoPDFviewer has been modified to directly open files using 'open', which knows how to automatically convert PostScript files. This problem prevented viewing of output from drawtree and drawgram.
Sequin has been upgraded to version 10.0.
Bluejay has been upgraded to version 1.3.
ACeDB is now considered a legacy application, and will be replaced with a different lightweight database system in a future release. This is partly because the code was compiled on a 32-bit Linux system in 2003 and is almost impossible to re-compile today. As a temporary fix, the scripts that launch xace or tace (birchdb, lbirchdb, l-gbirchdb and acedemo) have been upgraded to load 32-bit libraries included in lib-linux-intel or lib-linux-x86_64.
GDE has been frozen as a legacy application, and will no longer undergo development. The program will still work with all GDE menu files as of BIRCH 2.7, but future changes will only affect the biolegato family of programs. IN THE NEXT MAJOR RELEASE, GDE WILL BE DELETED FROM THE BIRCH SYSTEM.