Info messages

• Python part largely rewritten
• More informative messages generated in output
• Base functionality for using iqtree as alternative tree builder; this is not available to the user because the number of recombinations predicted by iqtree is far beyond expectations
• Made sure all tests are run, including integration tests

Docker build

This release is created to get a recent image with software version number onto DockerHub. No changes to the code.

v2.3.4: Dynamically allocate memory

This should fix the common problem of segmentation faults, which occur on alignments with a large number of SNPs and are due to stack overflow.

v2.3.3: independent dockerfile

Merge pull request #226 from puethe/independent_docker

Dockerfile independent from debian package

v2.3.2: updated installation instruction, fixes and improved argument handling

• improve handling of several arguments that have a fixed set of possible values
• update of installation instruction
• fix of test suite
• remove gubbins_drawer

Output a tree with the internal nodes labelled

v2.3.1

Merge branch 'internal_nodes'

Gubbins Drawer updates

Merge pull request #201 from andrewjpage/gubbins_drawer_help

Gubbins drawer help text

Fix default extended help text

Merge pull request #200 from andrewjpage/helptext

Fix default extended help text.

Allow the use of RAXML AVX2 binaries

Allow the use of RAXML AVX2 binaries

Remove use of Biopythons sub_features function which has been deprecated.

Remove use of Biopythons sub_features function which has been deprecated.