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Martinsos
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opal
SIMD C/C++ library for massive optimal sequence alignment (local/SW, infix, overlap, global)
MIT License
35
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10
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Segmentation fault for certain gap open / gap extension configuration
#33
michal-kierzynka
opened
1 year ago
0
Refactor SIMD code and add support for SSE2 and NEON
#32
althonos
opened
2 years ago
1
Add E-value
#31
Martinsos
opened
8 years ago
0
no member named 'abs' in namespace 'std';
#30
FadelBerakdar
opened
8 years ago
1
Add SHW mode
#29
Martinsos
opened
9 years ago
0
When gap open is smaller then gap extend, stuff breaks
#28
Martinsos
opened
9 years ago
0
Add flag for turning off overflow check
#27
Martinsos
opened
9 years ago
0
report GCUPS for opal_aligner ?
#26
jeffdaily
closed
9 years ago
3
Alignment of data for SSE/AVX does not seem to matter
#25
Martinsos
opened
9 years ago
0
deleted
#24
Martinsos
closed
9 years ago
0
Improve speed of basic search
#23
Martinsos
opened
9 years ago
4
Automatize comparison with other aligners and performance tests
#22
Martinsos
closed
9 years ago
0
Create example of usage
#21
Martinsos
opened
9 years ago
0
Update README!
#20
Martinsos
opened
9 years ago
0
Split swimd.cpp into more files
#19
Martinsos
opened
9 years ago
0
Limit memory usage of alignment
#18
Martinsos
opened
9 years ago
0
Improve alignment speed
#17
Martinsos
opened
9 years ago
3
Consider using swimd to solve 1:1 for large targets
#16
Martinsos
opened
9 years ago
0
Make function input more flexible
#15
Martinsos
closed
9 years ago
1
Add flag to choose if end location is needed (to make search faster)
#14
Martinsos
closed
9 years ago
1
Implement finding location in target and query where best score was found
#13
Martinsos
closed
9 years ago
1
Difference between swimd and edlib
#12
rob-p
closed
10 years ago
2
Slowdown after new feature
#11
Martinsos
closed
9 years ago
2
scores are often incorrect
#10
tolot27
closed
10 years ago
11
calculate hits for all query sequences of a multiple fasta file
#9
tolot27
opened
10 years ago
1
fixed all warnings; set -Wall; changed alphabet to unsigned char*
#8
tolot27
closed
10 years ago
1
made parameters as compatible as possible with NCBI Blast; fixes #6
#7
tolot27
opened
10 years ago
2
make command line parameters compatible to blast/swipe
#6
tolot27
opened
10 years ago
2
Add callback function that is called after sequence is calculated
#5
Martinsos
opened
10 years ago
0
Write better tests
#4
Martinsos
opened
10 years ago
0
Process multiple cells in one iteration, add padding to database sequences, optimize for cache
#3
Martinsos
opened
10 years ago
3
Implement AVX2 version
#2
Martinsos
closed
10 years ago
1
Implement calculation of alignment
#1
Martinsos
closed
9 years ago
6