| Online Tool | Description |
|---|---|
| @ Primer Design Tools | |
| 3DNA | Software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures |
| AmiGene | Annotation of Microbial Genes for for automatically identifying the most likely CoDing Sequences (CDSs). |
| BLAST Search of Nucleotide, Protein and Genome Databases | Compare your query sequence to the working draft sequence of the human genome or its mRNA and protein products. |
| Biology WorkBench | Protein tools: structure prediction, blast, multiple sequence alignment, randomize sequence. Nucleic tools: Primer design. |
| CD-HIT | A series of programs for sequence comparisons. Creating non-redundant datasets for proteins. Clustering analysis of various types of DNAs and RNAs. Clustering 16S rRNA tags into OTUs (454, Iontorrent and Illumina reads). Generate protein families. Merge assembled contigs. |
| ConSeq Server | Server for the identification of functionally and structurally important residues in protein sequences. |
| Countcodon | Generates a codon usage table for the input sequence. |
| Cpgreport | Identify and report CpG islands in nucleotide sequences. |
| EMBOSS Seqret | Sequence format conversion. Reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions. |
| FMAP | Sequence alignment with genome. Maps sequence to human, rat and mouse genomes. |
| GeneMark | Gene Prediction in Bacteria, Archaea and Metagenomes. |
| Genscan | Predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. |
| MEME Suite | Motif-based analysis of DNA, RNA and protein sequences. |
| NEBcutter | Examines DNA sequence to find large, non-overlapping open reading frames (ORFs) and sites for all restriction enzymes that cut the sequence just once. |
| ORF Finder | ORF Finder (Open Reading Frame Finder). |
| PROMALS3D | Alignments for multiple protein sequences or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures. |
| Pictogram | Tool to visualize sequence alignments and consensus sequences showing the relative frequencies of the bases at each position. |
| PlasMapper | Generates and annotates plasmid maps using only plasmid DNA sequence as input. Figures may be rendered in PNG, JPG, SVG or SVGZ format. |
| PromoSer | Web-based service for extraction of a large number of promoter sequences from mammalian genomes. |
| RNA/DNA secondary structure prediction and design | PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules. |
| Restriction Map Generator | Analyzes a DNA sequence to identify Restriction Enzyme Sites and generate a comprehensive map overview of their locations within the DNA sequence. |
| Restriction Mapper | Maps sites for restriction enzymes (restriction endonucleases) in DNA sequences. |
| SOAP Short Oligonucleotide Analysis | Program for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis. |
| Sequence Manipulation Suite | JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. |
| Superlink | Genetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs. |
| TFBIND | Searching transcription factor binding sites (TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS). |
| TRACTS | A program to map oligopurine.oligopyrimidine and other binary DNA tracts. |
| Trait-o-matic | Open-source tool to find and classify phenotypic correlations for variations in whole genomes. |
| VIROME | Classification of predicted open-reading frames (ORFs) from viral metagenomes. |
| Vista | Programs and databases for comparative analysis of genomic sequences. |
| WEGO | Web Gene Ontology Annotation Plot. |
What is Sequence Analysis for Mac. Sequence Analysis is sequence editing, reverse complement, protein translation, ORF finding, secondary structure, composition, isoelectric point, primer design, pairwise comparison, publish layout and sequence reformatting. Fetches sequence entries directly from the NCBI via Accession number or GID.
Developer: Tom Hall
Supported platforms: Windows 95 and higher
- It enables them to perform end-to-end reproducible data analyses using a free standalone desktop application (available on Windows, Mac and Linux). Unlike existing tools (e.g. Galaxy), the Graphical User Interface (GUI)-based easyfm is not dependent on any high-performance computing (HPC) system and can be operated without an internet connection.
- Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations. MEGA 11.0.8 for Windows and Linux(32 and 64 bit) and macOS is now available. This is a bug fix release and is the first stable release of version 11.
Illumina Sequencing Analysis Viewer Download
Download: http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Features
View Quality scores
No
View raw data
Yes
Assembly
Yes, but you have to manually align up each sequence and manually create a consensus sequence (which other programs are very good at).
Input file formats
ABI files (.abi and .ab1), FASTA, Genbank, Fasta, Phylip 3.2, Phylip 4, GCG, Clustal, and NBRF/PIR formats (a complete list can be found in the manual).
Output file formats
Celsa practice test pdf. ABI files, text files, FASTA, Genbank, Fasta, Phylip 3.2, Phylip 4, GCG, Clustal, and NBRF/PIR formats (a complete list can be found in the manual).
Trimming
No trimming of low quality regions
Integrated Blast
Yes
Sequence Analysis Tools
Open multiple windows
Sanger Sequencing Analysis Tools
Yes Solidworks 2017 free.
Edit bases
Yes
ABI limits (regions outside of clear range region are displayed in grey)
No
Other functions
- Reverse complement sequence
- Rudimentary phylogenetic tree viewer
- Plasmid drawing and restriction site mapping
- Translation
- ClustalW multiple sequence alignment
A complete list can be found on the BioEdit website
Cost
Free, but no longer maintained. Etka 8.0 download free. The website seems to also be down these days. We have a copy of the installer if anyone wants to get a copy.
Comments
Sequence Analysis Viewer Download
BioEdit is free and provides many basic functions for protein and nucleic sequence editing, alignment, manipulation and analysis. The software works is no longer maintained. If you only need a trace viewer or want to do basic editing other free software options are better because they have more trimming options and display the quality values (phred scores). However, if you are looking for a free alignment program BioEdit might be right for you.