v2.3.2 - 12 Jan 2018
-----
Update installation instructions to remove all reference to HomeBrew.

v2.3.1 - 22 Sept 2017
-----
Output a tree with the internal nodes labelled.

v2.3.0 - 21 Sept 2017
-----
Add helptext to gubbins drawer and require tree as a positional argument rather than an option.

v2.2.3 - 15 Sept 2017
-----
Fix default extended help text.

v2.2.2 - 4 Sept 2017
-----
Allow the use of RAXML AVX2 binaries. 

v2.2.1 - 20 Feb 2017
-----
Remove use of Biopythons sub_features function which has been deprecated.

v2.2.0 - 31 Oct 2016
------
By default dont filter out sequences which are 100% identical.

v2.1.0 - 22 July 2016
------
Use GTRCAT model by default in RAxML instead of GTRGAMMA (massive speedup).
C code optimisations in Gubbins.

v2.0.0 - 26 May 2016
------
Reconstruct internal sequences by default using RAxML rather than fastML. 
Addresses speed issues raised by users. 
RAxML version 8 now required as a minimum.
Remove pairwise support since RAxML wont support it. Need at least 4 genomes as input.

v1.4.10 - 31 Oct 2016
------
Backport a change so that by default dont filter out sequences which are 100% identical.

v1.4.9 - 15 Apr 2016
------
If sequences are 100% identical, filter out duplicates.
Refactor Python FASTA validation to separate file.

v1.4.8 - 12 Apr 2016
------
Fix to lookup of CPU instruction sets to decide which versions of RAxML are supported. Provided by aaronk.

v1.4.7 - 29 Feb 2016
------
Fix allocation from stack bug (from jeromekelleher). For large numbers of SNPs allocating from the stack caused a segfault. 
This fixes the issue by allocating from the heap with malloc.

v1.4.6 - 29 Feb 2016
------
Added back midpoint rerooting as the default. Was the default up to v1.3.5 (25/6/15) and was removed by mistake. 
It didnt effect the recombination detection, just the tree didnt look as pretty at the end.

v1.4.5 - 13 Jan 2016
------
Removed the install.sh file which gets regenerated automatically when the code is built, 
but if its there already it can cause problems on some platforms.

v1.4.4 - 9 Dec 2015
------
Debian reported that Gubbins failed to build on one platform. These changes fix this bug and 
cleaned up some other build issues to make it easier to compile on OSX from source.

v1.4.3 - 19 Nov 2015
------
The Debian directory was removed because it now lives in its own repository in the Debian world.

v1.4.2 - 2 Sept 2015
------
If filenames are too long, RAxML crashes. To avoid this a hard limit was introduced, and Gubbins exits with an error message.

v1.4.1 - 7 Jul 2015
------
Update Brew installation instructions and python dependancy versions.

v1.4.0 - 1 Jul 2015
------
Update from python 2 to python 3. This is to allow for inclusion in Debian (because they dont accept python 2 anymore). 
Also detect fastml version and modify parameters as required.



Changes prior to May 2015
=========
gubbins (1.3.4~trusty1) trusty; urgency=low

  * Identify blocks at end of genome

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 18 Apr 2015 14:51:00 +0000

gubbins (1.3.3~trusty1) trusty; urgency=low

  * Max window size arg bug

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 16 Apr 2015 16:09:00 +0000

gubbins (1.3.2~trusty1) trusty; urgency=low

  * pass in self to window size check

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 16 Apr 2015 16:00:00 +0000

gubbins (1.3.1~trusty1) trusty; urgency=low

  * Calculate bases used for clonal frame

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 16 Apr 2015 15:00:00 +0000

gubbins (1.3.0~trusty1) trusty; urgency=low

  * Apply filtering to leaf nodes

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 14:17:00 +0000

gubbins (1.2.5~trusty1) trusty; urgency=low

  * Block out SNPs from downstream recombinations

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 14:17:00 +0000

gubbins (1.2.4~trusty1) trusty; urgency=low

  * Python verion number in script

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 14:17:00 +0000


gubbins (1.2.3~trusty1) trusty; urgency=low

  * Eggs werent included in deb

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 14:17:00 +0000


gubbins (1.2.2~trusty1) trusty; urgency=low

  * Last sequence wasnt in array

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 14:17:00 +0000

gubbins (1.2.1~trusty1) trusty; urgency=low

  * Update VCF and EMBL output formats

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 11:36:00 +0000

gubbins (1.2.0~trusty1) trusty; urgency=low

  * Dont fill in parent bases with gaps from children

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 30 Mar 2015 10:16:00 +0000

gubbins (1.1.2~trusty1) trusty; urgency=low

  * Fix GFF formatting and C warnings

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 23 Jan 2015 16:02:00 +0000

gubbins (1.1.1~trusty1) trusty; urgency=low

  * Message to tell user theres a problem with outgroups not a clade

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 23 Jan 2015 16:02:00 +0000

gubbins (1.1.0~trusty1) trusty; urgency=low

  * Allow for multiple outgroups

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 23 Jan 2015 15:05:00 +0000

gubbins (1.0.12~trusty1) trusty; urgency=low

  * Remove internal labels from final tree

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 20 Jan 2015 09:03:00 +0000

gubbins (1.0.11~trusty1) trusty; urgency=low

  * Test inputs contain variation

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 19 Jan 2015 09:01:00 +0000

gubbins (1.0.10~trusty1) trusty; urgency=low

  * Upload failed on ubuntu

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 19 Jan 2015 09:01:00 +0000

gubbins (1.0.9~trusty1) trusty; urgency=low

  * Remove cpu info and manually look for the flag

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 6 Jan 2015 14:09:00 +0000

gubbins (1.0.8~trusty1) trusty; urgency=low

  * Limit the cpu info lookup to get around bug in ubuntu build

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 8 Dec 2014 12:58:00 +0000

gubbins (1.0.7~trusty1) trusty; urgency=low

  * Update rho/theta calculation to blocks/snps outside recombinations

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 8 Dec 2014 12:58:00 +0000

gubbins (1.0.6~trusty1) trusty; urgency=low

  * Drawer allow for variation tag

 -- Andrew Page <ap13@sanger.ac.uk>  Wed, 3 Dec 2014 11:32:00 +0000

gubbins (1.0.5~trusty1) trusty; urgency=low

  * Fasttree executables with upper and lower case

 -- Andrew Page <ap13@sanger.ac.uk>  Wed, 19 Nov 2014 14:16:00 +0000

gubbins (1.0.4~trusty1) trusty; urgency=low

  * Warning when number of threads changed for raxml

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 14 Nov 2014 14:16:00 +0000

gubbins (1.0.3~trusty1) trusty; urgency=low

  * Dont use multiple threads for raxml if not requested

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 14 Nov 2014 14:16:00 +0000

gubbins (1.0.2~trusty1) trusty; urgency=low

  * Allow for more convergence methods

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 14 Oct 2014 14:16:00 +0000

gubbins (1.0.1~trusty1) trusty; urgency=low

  * Fixed unstable python test

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 14 Oct 2014 14:16:00 +0000

gubbins (1.0~trusty1) trusty; urgency=low

  * Strict convergence option

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 14 Oct 2014 14:16:00 +0000

gubbins (0.6~trusty1) trusty; urgency=low

  * Gubbins drawer can now use .embl file with recombination regions

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 9 Sep 2014 13:03:00 +0000

gubbins (0.5~trusty1) trusty; urgency=low

  * Thread support for RAXML

 -- Andrew Page <ap13@sanger.ac.uk>  Tue, 9 Sep 2014 09:45:00 +0000

gubbins (0.4.1~trusty1) trusty; urgency=low

  * Check for FastTree lowercase executable

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 8 Sep 2014 10:32:00 +0000

gubbins (0.4~trusty1) trusty; urgency=low

  * Rename output files for pairwise comparison

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 5 Sep 2014 10:26:00 +0000

gubbins (0.3~trusty1) trusty; urgency=low

  * Changes statistics file output

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 4 Sep 2014 17:07:00 +0000

gubbins (0.2~trusty1) trusty; urgency=low

  * Rename final output files

 -- Andrew Page <ap13@sanger.ac.uk>  Mon, 1 Sep 2014 16:44:00 +0000

gubbins (0.1.11~trusty1) trusty; urgency=low

  * Python remove internal node names if passed in as a starting tree

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 22 Aug 2014 16:44:00 +0000

gubbins (0.1.10~trusty1) trusty; urgency=low

  * Python print list of excluded sequences to STDOUT by default

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 22 Aug 2014 14:44:00 +0000

gubbins (0.1.9~trusty1) trusty; urgency=low

  * Python prints error messages for invalid sequence files and sends exit code 1

 -- Andrew Page <ap13@sanger.ac.uk>  Fri, 22 Aug 2014 10:37:00 +0000

gubbins (0.1.8~trusty1) trusty; urgency=low

  * Python fastml exec fix
  * Python check sequence names in tree

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 15 Aug 2014 16:32:00 +0000

gubbins (0.1.7~trusty2) trusty; urgency=low

  * Package for trusty
  * Move blocks further inwards

 -- Andrew Page <ap13@sanger.ac.uk>  Thu, 14 Aug 2014 09:56:00 +0000

gubbins (0.1.6) saucy; urgency=low

  * Changed build depends

 -- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org>  Wed, 26 Jun 2014 14:46:07 +0000

gubbins (0.1.5) saucy; urgency=low

  * Updated build system and removed some tests

 -- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org>  Wed, 25 Jun 2014 14:46:07 +0000

gubbins (0.1.4) saucy; urgency=low

  * Updated Debian packages such that the build version is taken from Automake.

 -- Aidan Delaney (Packaging Key) <aidan@ontologyengineering.org>  Mon, 31 Mar 2014 14:46:07 +0000