Category
page 1Bioinformatics algorithms
sequence alignment
process in bioinformatics that aligns (identifies equivalent sites within) molecular sequences
BLAST
bioinformatics software
Needleman–Wunsch algorithm
algorithm
Smith–Waterman algorithm
algorithm performs local sequence alignment
neighbor joining
clustering method in bioinformatics
UPGMA
UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. It also has a weighted variant, WPGMA, and they are generally attributed to Sokal and Michener.
Baum–Welch algorithm
algorithm
sequence mining
data mining technique
Hirschberg's algorithm
algorithm
Ukkonen's algorithm
algorithm for construction of suffix trees
SAMtools
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. Both simple and advanced tools are provided, supporting complex tasks like variant calling and alignment viewing as well as sorting, indexing, data extraction and format conversion. SAM files can be very large (tens of Gigabytes is common), so compression is used to save space. SAM files are human-readable text files, an
complete-linkage clustering
agglomerative hierarchical clustering method