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torognes
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swipe
Smith-Waterman database searches with inter-sequence SIMD parallelisation
GNU Affero General Public License v3.0
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Create CITATION.cff
#39
frederic-mahe
opened
9 months ago
0
Show all descriptions and alignments with maximum score
#38
krdav
opened
1 year ago
3
Show all descriptions and alignments with maximum score
#37
krdav
opened
1 year ago
0
support on ARM64
#36
jianshu93
opened
2 years ago
1
arm64?
#35
gaboentropy
closed
2 years ago
2
swipe crashes with uniclust30_2018_10 and a SCOP sequence
#34
konstin
closed
2 years ago
6
Now in homebrew
#33
tseemann
opened
5 years ago
1
compilation warnings with GCC 7 and GCC 8
#32
frederic-mahe
opened
6 years ago
1
Segfault on databases in recent NCBI format
#31
torognes
closed
6 years ago
1
Fix compilation errors when using C++11
#30
unisolate
closed
7 years ago
1
Add matrix support for DNA/DNA ( blastn ) searches
#29
rmhubley
opened
8 years ago
1
Crash when searching long nucleotide sequences
#28
torognes
closed
8 years ago
1
some database functions return incorrect length
#27
tolot27
opened
10 years ago
0
Internal error in align function under certain circumstances
#26
torognes
closed
10 years ago
3
let run the alignment thread(s) in parallel to the search threads
#25
tolot27
opened
10 years ago
0
use lock-free queue for hit_list
#24
tolot27
opened
10 years ago
1
Dual affine gap penalties
#23
torognes
opened
10 years ago
0
Internal error in align function when using a custom substitution matrix
#22
torognes
closed
10 years ago
3
Improve checking of FASTA-formatted files and handle lines starting with #
#21
torognes
opened
10 years ago
1
Crash and worse problems when running mpiswipe on Archlinux
#20
torognes
closed
10 years ago
2
Output results in SAM or BAM format
#19
torognes
opened
10 years ago
1
Use a FASTQ file as query input
#18
torognes
opened
10 years ago
2
mpiswipe won't run with some variants of MPI
#17
torognes
opened
10 years ago
1
Segmentation fault with large nucleotide databases and many alignments
#16
torognes
closed
10 years ago
3
Documentation!
#15
torognes
opened
10 years ago
0
Fallback to non-SIMD code if SIMD not present (or as an option)
#14
torognes
opened
10 years ago
0
Show all significant alignments per sequence, not just the single best
#13
torognes
opened
10 years ago
0
Allow zero gap opening or gap extension penalty
#12
torognes
opened
10 years ago
0
Optionally output the raw alignment score, not just the bit score
#11
torognes
opened
10 years ago
2
no similarities of long sequences are computed
#10
tolot27
closed
10 years ago
2
Check behaviour when -z option argument is not an integer
#9
torognes
closed
10 years ago
0
Add option to use the new sequence length adjustment statistics (FSC) in BLAST 2.2.26 and later
#8
torognes
opened
11 years ago
0
Add option (-z) to set effective database size
#7
torognes
closed
11 years ago
1
Adapt to AVX2
#6
torognes
opened
11 years ago
1
Search with a query sequence profile
#5
torognes
opened
11 years ago
0
Check compatibility with new versions of preformatted databases from NCBI
#4
torognes
closed
11 years ago
1
Fix random crashes with "Internal error in align function"
#3
torognes
closed
10 years ago
1
Make BLAST compatible XML output format
#2
torognes
opened
11 years ago
0
Compile on Mac
#1
torognes
closed
11 years ago
1