Version 3.4.0

• Added a simple sequence simulator for testing
• Fixed an issue where aligning the same set of sequences with different number of threads would result in slightly different alignments.

Minor feature update

Kalign now detects and ignores empty entries in fasta inputs.

Version 3.3.4: switched to cmake

Switched to cmake
Additional changes:

1. added a Kalign library to make it easier to use Kalign from another projects
2. added a block version of Gene Myers bit parallel string matching code (described here: Myers, Gene. "A fast bit-vector algorithm for approximate string matching based on dynamic programming." Journal of the ACM (JACM) 46.3 (1999): 395-415). This means Kalign will now run equivalently on processors with and without AVX2 instructions (e.g. apple M1 / M2 and ARM chips).
3. alignment types giving users more control over alignment parameters.
4. multi-threading

Kalign v3.3.2

version 3.3.2 - Bug Fix

There was a bug in building a guide tree from highly similar sequences. The fix
involved distributing identical sequences equally among branches. The problem only happened
in cases when there were thousands of identical sequences.

In addition Kalign now compiles on Apple's M1 chip and possibly on other ARM architectures
as well (although I did not test the latter).

v3.3.1 - Minor improvements

The previous version kalign checked the top 50 sequences in inputs to determine
whether the sequences are aligned or not. If the first 50 sequences are not aligned
but following sequences contain gaps (or other characters!) kalign can crash. In this
version (3.3.1) kalign checks all sequences, thereby avoiding this issue.
To alert users to the situation described above and to warn users about the presence of
odd characters, kalign now produces a warning message like this:

[Date Time] : LOG : Start io tests.
[Date Time] : LOG : reading: dev/data/a2m.good.1
[Date Time] : LOG : Detected protein sequences.
[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 505)
[Date Time] : WARNING : The input sequences contain gap characters: (rwalign.c line 506)
[Date Time] : WARNING : "-" : 36 found (rwalign.c line 510)
[Date Time] : WARNING : BUT the sequences do not seem to be aligned! (rwalign.c line 514)
[Date Time] : WARNING : (rwalign.c line 515)
[Date Time] : WARNING : Kalign will remove the gap characters and (rwalign.c line 516)
[Date Time] : WARNING : align the sequences. (rwalign.c line 517)
[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 518)

v3.3 - Multi-threading

Kalign now runs pairwise distance estimation, guide tree building and alignments in parallel.
Memory optimisations.
Optimised bi-sectional K-means algorithm.
added -clean option to check for sequences with identical names but different sequences.
fixed minor bug in alignment I/O module

v3.2.3

Replaced timing code.

v3.2.2

Minor bugs fixed. Including:

• bug in alignment write test

v3.2.0

Added support for reading sequences from standard input:

	cat file.fasta | kalign -f fasta | ....

Added support for combining multiple input files into one alignment:

	kalign sequencesA.fa sequencesB.fa > msa.fa

Also works in combination:

	cat file.fasta | kalign sequencesA.fa sequencesB.fa > msa.fa

Minor:
- added m4 macros to enable / disable compiler flags
- added m4 macro for valgrind. Now there is a make target
called check-valgrind that run all tests through valgrind.

v3.1.1 - Minor bug fixes

• fixed some installation issues on macOS