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Make BLAST compatible XML output format

enhancement

Status: Open.

#2 In torognes/swipe;

· torognes opened on Feb 19, 2013

Search with a query sequence profile

enhancement

Status: Open.

#5 In torognes/swipe;

· torognes opened on Feb 19, 2013



Adapt to AVX2

enhancement

Status: Open.

#6 In torognes/swipe;

· torognes opened on Feb 19, 2013

1 comment



Add option to use the new sequence length adjustment statistics (FSC) in BLAST 2.2.26 and later

enhancement

Status: Open.

#8 In torognes/swipe;

· torognes opened on Apr 30, 2013



Optionally output the raw alignment score, not just the bit score

enhancement

Status: Open.

#11 In torognes/swipe;

· torognes opened on Jan 15, 2014

2 comments

Allow zero gap opening or gap extension penalty

enhancement

Status: Open.

#12 In torognes/swipe;

· torognes opened on Feb 13, 2014



Show all significant alignments per sequence, not just the single best

enhancement

Status: Open.

#13 In torognes/swipe;

· torognes opened on Feb 13, 2014

Fallback to non-SIMD code if SIMD not present (or as an option)

enhancement

Status: Open.

#14 In torognes/swipe;

· torognes opened on Feb 13, 2014



Documentation!

enhancement

Status: Open.

#15 In torognes/swipe;

· torognes opened on Feb 13, 2014



mpiswipe won't run with some variants of MPI

enhancement

Status: Open.

#17 In torognes/swipe;

· torognes opened on Mar 10, 2014

1 comment



Use a FASTQ file as query input

enhancement

Status: Open.

#18 In torognes/swipe;

· torognes opened on Mar 27, 2014

2 comments

Output results in SAM or BAM format

enhancement

Status: Open.

#19 In torognes/swipe;

· torognes opened on Mar 27, 2014

1 comment

Improve checking of FASTA-formatted files and handle lines starting with #

enhancement

Status: Open.

#21 In torognes/swipe;

· torognes opened on May 6, 2014

1 comment

Dual affine gap penalties

enhancement

Status: Open.

#23 In torognes/swipe;

· torognes opened on May 23, 2014

use lock-free queue for hit_list

Status: Open.

#24 In torognes/swipe;

· tolot27 opened on Jun 26, 2014

1 comment

let run the alignment thread(s) in parallel to the search threads

Status: Open.

#25 In torognes/swipe;

· tolot27 opened on Jun 26, 2014

some database functions return incorrect length

Status: Open.

#27 In torognes/swipe;

· tolot27 opened on Jul 29, 2014

Add matrix support for DNA/DNA ( blastn ) searches

Status: Open.

#29 In torognes/swipe;

· rmhubley opened on Aug 4, 2016

1 comment

compilation warnings with GCC 7 and GCC 8

Status: Open.

#32 In torognes/swipe;

· frederic-mahe opened on May 6, 2018

1 comment

Now in homebrew

Status: Open.

#33 In torognes/swipe;

· tseemann opened on Oct 5, 2018

1 comment

support on ARM64

Status: Open.

#36 In torognes/swipe;

· jianshu93 opened on Jul 14, 2022

1 comment

Show all descriptions and alignments with maximum score

Status: Open.

#37 In torognes/swipe;

· krdav opened on Aug 14, 2023