webchem.ncbr.muni.cz - Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized...
github.com - Kalign is a fast multiple sequence alignment program for biological sequences.
Align sequences and output the alignment in MSF format:
kalign -i BB11001.tfa -f msf -o out.msf
Align sequences and output the alignment in clustal format:
kalign...
mulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...
www.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...
clark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...
github.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...
www.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite
Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...
compbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:
Reading a pre-existing reference...
hciweb.iwr.uni-heidelberg.de - This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit,...