Online webserver and pipelines

You can test MACSE online (release v2.01b) using the MBB webser. The previous version is still available: old 0.9b1 release. All pipelines source code are provided on the dedicated github repository.

Latest release of MACSE

MACSE release 2.07
march 2023
The most recent release of MACSE Fix a bug in trimAlignment sub-program

This release of MACSE is also available through conda on the anaconda repository.

Latest release of pipelines based on MACSE

april 2020
The container is now published on the official singularity hub ( omm_macse) and docker hub (omm_macse)
Add prank to the list of third party AA aligners
Improve parameter parsings, error messages and temporary file management
Fix some bugs so that traceability files are produced even in absence of (pre) filtering
By default, during filtering, sites with nucleotides for less than 4 sequences are now kept, and this can be adjusted using a new parameter « min_seqToKeepSite »
The corresponding singularity recipe
december 2019
Singularity container providing an alignment pipeline relying on MACSE. This pipeline is slower but should lead to better alignment in case of numerous frameshifts (e.g. for dataset containing pseudogenes). For large dataset containing sequences where frameshifts are expected to be rare the OMM_pipeline is probably better suited (require singularity > 3.3)
The corresponding singularity recipe

Macse release history (and associated jar files)

MACSE release 2.06
january 2022
The most recent release of MACSE
Minor bug fix related to the alphabet option, more information here.
MACSE release 2.05
october 2020
The most recent release of MACSE
This release includes some additional genetic codes: codes 21 to 33 of the NCBI.
We also included an extra genetic codes to better handle seleno proteins. When using this seleno protein code, the TGA codon is translated by MACSE into a Cysteine instead of a STOP.
release 2.04
september 2020
This release fixes a small bug in the exportAlignment subprogram (some internal frameshifts/stops were not replaced)
release 2.03
september 2018
Previsous v2 releases were not compatible with java 9 and above, this release fixes this compatibility issue
release 2.01
july 2018
Minor improvements and bug fixes
Improve the readibility of command line help
In case of incorrect command line arguments, the error message was correctly printed on windows not on linux, fixed
Add an option to exportAlignment to preserve gap only sites
New trimSequences sub program
release 2.00
june 2018
Major update
Improved version of the initial algorithm to increase alignment speed
New subprogram to remove non-homologous sequence fragments before alignment
Newly designed graphical interface providing a user-friendly access to the different subprograms
New detailed user documentation with basic tutorials
release 1.2
may 2016
Speed improvement for linux OS (simply removing calls to currentTimeMillis() used for internal performance check,
New functionalities (e.g. consensus sequence)
Less verbose (output statistics of genetic code usage instead of full list …)
release 1.01b
february 2014
Minor improvement in the splitAlignment subprogram. Taxa indicated in the subset list are now ignored if they are not present in the original alignment. This allow to run the same command line and same subset list to split multiple alignment files containing different set of sequences/taxa.
release 1.01
july 2013
MACSE now provides a full toolkit dedicated to coding sequence alignments. This toolkit allows us to reliably align thousands of COI and matK sequences in a barcoding context (see our barcoding subproject web page for further information).
Here are some of the functionalities provided by the various subprograms included in MACSE:
– Enriching an existing alignment with additional sequences
– Refining an existing alignment
– Splitting an existing alignment keeping a subset of sites and/or sequences
– Formatting and exporting an alignment (e.g. by removing or masking codons containing frameshifts)
– Translating a nucleotide alignment into an amino acid alignment
– …
For usage examples see MACSE tutorial and download associated examples.
release 0.9b1
september 2012
Improvement of memory management
Several corrections of small bugs
release 0.8b2
september 2011
First release of MACSE associated to the original PLoS One publication

Pipeline release history

october 2019
Singularity container providing the alignment pipeline developped to obtain OrthoMaM alignments (require singularity > 3.3)
The corresponding singularity recipe
The first part of the release number (here 10) refer to the OrthoMaM release for which this pipeline was developped