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DNA Alignment Segment-based method for intraspecific alignments: Both: Local (preferred) or Global: A.Roehl: 2005 (latest version 2008) DNA Baser Sequence Assembler Multi-alignment; Full automatic sequence alignment; Automatic ambiguity correction; Internal base caller; Command line seq alignment: Nucleotides: Local or global: Heracle BioSoft SRL
Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built-in algorithms, mutation detection, including detection of heterozygous single-nucleotide polymorphism, analysis of heterozygous insertions and ...
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.
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
SOAP (Short Oligonucleotide Analysis Package) is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [25 ...
Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platform: Public domain: National Center for Biotechnology Information: CP2K: Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. Linux, macOS, Windows: GPL and LGPL
List of proprietary bioinformatics software; List of open-source bioinformatics software; Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: Sequence analysis software. List of sequence alignment software; List of alignment visualization software; Alignment-free sequence analysis
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