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2. List of sequence alignment software - Wikipedia

   en.wikipedia.org/wiki/List_of_sequence_alignment...

   Alignment of cDNA sequences to a genome. Nucleotide DECIPHER: Alignment of rearranged genomes using 6 frame translation: Nucleotide FLAK Fuzzy whole genome alignment and analysis: Nucleotide GMAP Alignment of cDNA sequences to a genome. Identifies splice site junctions with high accuracy. Nucleotide Splign Alignment of cDNA sequences to a genome.

3. List of alignment visualization software - Wikipedia

   en.wikipedia.org/wiki/List_of_alignment...

   This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general understanding of large-scale DNA or protein alignments; Visualize alignments for figures and publication; Manually edit and curate automatically generated alignments; Analysis in depth

4. SAMtools - Wikipedia

   en.wikipedia.org/wiki/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.

5. List of phylogenetics software - Wikipedia

   en.wikipedia.org/wiki/List_of_phylogenetics_software

   EzEditor is a java-based sequence alignment editor for rRNA and protein coding genes. It allows manipulation of both DNA and protein sequence alignments for phylogenetic analysis: Multiple sequence alignment and editing: Y.-S. Jeon, K. Lee, S.-C. Park, B.-S. Kim, Y.-J. Cho, S.-M. Ha, and J. Chun fastDNAml Optimized maximum likelihood ...

6. Bowtie (sequence analysis) - Wikipedia

   en.wikipedia.org/wiki/Bowtie_(sequence_analysis)

   Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. [3] The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms.

7. HMMER - Wikipedia

   en.wikipedia.org/wiki/HMMER

   A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.