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2023-12-10 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.4.0
- Added a simple sequence simulator for testing
- Fixed an issue where alignments would be slighly different
depending on the number of threads used.
2022-11-05 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.3.5
- Added a check to find and remove sequences of length 0.
2022-10-28 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.3.4 - Cmake and more
- switched to cmake
Added:
1) a Kalign library to make it easier to use Kalign from another projects
2) 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
2022-03-21 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.3.2 - Bug Fix
There was a bug in building a guide tree from highly similar sequences. The fix
was involved distributing identical sequences equally among branches. This only happened
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).
2021-04-16 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.3.1 - Bug Fix
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)
2020-11-06 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.3 - Threading and more
- 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
2020-09-24 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.2.7 - Development version
- dynamic programming in now more modular.
- fixed rare bug in alignment input / output
- added gap parameters (--gpo, --gpe, --tgpe)
- for protein alignment I now use the CorBLOSUM66_13plus matrix from:
Hess M, Keul F, Goesele M, Hamacher K.
Addressing inaccuracies in BLOSUM computation improves homology search performance.
BMC bioinformatics. 2016 Dec 1;17(1):189.
with the empirically derived gap penalties.
2020-04-22 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.2.5
- Bug fix: when given long output named the first lines in msf
output could be truncated.
2020-04-01 Timo Lassmann <timo.lassmann@telethonkids.org.au>
* version 3.2.4
- Fixed issue relating to stdin input on clusters.
- Added more sanity checks
2020-03-16 Timo Lassmann
* version 3.2.3
- replaced timing code with code from the easel lib.
2020-02-23 Timo Lassmann
* version 3.2.2
- Fixed minor bug in rwaln test routine. It assumed that input alignments
were correctly formatted (which was not true for one test case). The
kalign executable was never affected by this.
- Added a script to test a few alignments.
2020-02-22 Timo lassmann
* version 3.2.1
minor bug fix removed "-lrt" required for old glibc versions and replaced
with a search in configure.ac: AC_SEARCH_LIBS([clock_gettime],[rt])
2020-02-15 Timo Lassmann
* version 3.2.0
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.
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