andi v0.14

This is a maintenance release of andi. Changes include

• New logdet evolutionary model. Thanks to @blueraleigh
• Fixed parsing error on fasta lines starting with -.
• Enabled compilation with pre-C11 compilers.
• Internal simplifications.

andi v0.13

This is a maintenance release. Changes include

• slightly improved performance
• rare bugs fixed
• faster file parsing
• better anchor threshold
• removal of psufsort, libdivsufsort is now mandatory
• fixed unit tests

andi v0.12

This release comes with a few changes to 0.11:

• implemented lucky anchors leading to a 10-15% speedup
• added progress indicator
• improved error messages
• corrected math
• various minor changes

Update 2018-03-26: Note that the unit tests may fail when executed in parallel. So please avoid that. 😅

andi v0.11

Besides minor improvements the changes include:

• new --file-of-filenames parameter
• new --truncate-names behaviour
• fixed anchor length computation
• zsh autocompletion (not yet installed)

andi v0.10

This release fixes a serious performance regression. Comparison of the 3085 S. Pneumoniae given in the paper now takes 4h and 59 min. Furthermore, warnings and errors were improved with all messages now being documented in the manual.

andi v0.9.6.2

This minor release fixes two issues on OS X:

• added missing header
• ignores __declspec from divsufsort headers
• TravisCI now also builds on OS X

Thanks to @tseemann for reporting.

andi v0.9.6.1

Due to my stupidity v0.9.6 printed nan instead of zeros on the main diagonal of bootstrapped matrices. This is now fixed.

andi v0.9.6

This release fixes the double JC correction and adds the Kimura two-parameter model. This can now be activate via the --model switch. Additionally, the unit tests are now reproducible.

andi v0.9.5

BUG: This version applies the JC correction twice.

This release adds pairwise bootstrapping to compute support values. Other changes include

• fixed two underflows
• fixed undefined behaviour
• improved warnings
• better input parsing
• better tests
• better docs with less typos

andi v0.9.4

Changes in this version include

• Previous builds with psufsort failed because of a missing file
• We now use pfasta to read FASTA files. It detects more errors than kseq.
• Added a compatibility library for missing functions
• The manual now has to be build by hand
• Improved build system and automatic tests

libdivsufsort is now also available as a package in Debian testing. It should be stable with the next release and is already in Ubuntu 15.10 (wily).