Most sequence alignment software comes with a suite which is paid and if it is free then it has limited number of options. Can anyone tell me the better sequence alignment software. Protein sequences can be reverse translated into DNA, compared using 'Dot-Plot' analysis and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats.
The DNASequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or. ...
- sequenceread-2.1.4.tar.gz
- sequenceread
- Freeware (Free)
- 171 Kb
- BSD; Linux
This tool will show the proportions between nucleotides in a DNA sequence.You don't need to install it or unpack it. Just download the program and double click to run it.
- Biology-tools-package.exe
- Heracle BioSoft
- Freeware (Free)
- 215 Kb
- Win95, Win98, WinME, WinNT 3.x, WinNT 4.x, Win2000, WinXP, Win2003, Linux, Mac OS X
Visit us for updated info: DNA Baser Assembler is easy to use software for simple and batch DNAsequence assembly, DNAsequence analysis, contig editing, metadata integration and mutation detection.
- DNA Baser Setup.exe
- Heracle BioSoft SRL
- Freeware (Free)
- 1.3 Mb
- Win95, Win98, WinME, WinNT 3.x, WinNT 4.x, Win2000, WinXP, Win2003, Win Vista, Win Vista x64, Linux, Mac OS X, Mac OS X 10.1, Mac OS X 10.2, Mac OS X 10.3, Mac OS X 10.4, Mac OS X 10.5, Mac Other
This 30 days fully functional demo of CLC DNA Workbench provides a wide range of advanced DNAsequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.Some analyses are:- Assembly of DNA. ...
- CLCDNAWorkbench.dmg
- CLC bio
- Freeware (Free)
- 52.6 Mb
- Mac OS X 10.4 or later
CLC DNA Workbench 5.6.1 provides users with a useful software environment enabling users to make a large number of advanced DNAsequence analyses, combined with smooth data management, and excellent graphical viewing and output options.Major. ...
- CLC DNA Workbench
- CLC bio A/S
- Trial ($990.00)
- Windows Vista, Windows XP, Windows 2000
Easy to use aligner software for DNAsequence contig assembly, contig editing, and mutation detection for Windows. It is a molecular biology software that can view and assemble sequences in contigs.Features: end clip, export, assemblies, detection. ...
- DNA BASER - affordablecontig assembly
- CubicDesign
- Shareware ($490.00)
- 1.11 Mb
- Windows
DNATREE is a computer program that simulates the branching of an evolutionary tree, using a model of random branching of lineages. It then evolves a DNAsequence along this tree, and displays the resulting sequences. The user can save the tree and. ...
- DNATREE for Mac OS X
- Joseph Felsenstein
- Freeware (Free)
- Mac OS X
DNA Replicator is a graphical tool (written in java) that compute the complementary sequence from an input DNAsequence. It's a really easy used. ...
- DNA Replicator
- dnarep
- Freeware (Free)
- 10 Kb
- Windows; Mac; Linux
SRF (Sequence Read Format) is used to store DNAsequence SRF (Sequence Read Format) is used to store DNA sequence data..
- srf-v0.1.tar.gz
- srf
- Freeware (Free)
- 840 Kb
- BSD; Linux
Swift is a DNAsequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped ...
- Swift Sequence AlignmentProgram
- pvg09
- Freeware (Free)
- 467 Kb
- Linux
jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website.jMOTU does the following: * reads input sequences in FASTA or NEXUS format * calculates distances between pairs of sequences using a combination of BLAST and the Needleman-Wunch exact global alignment algorithm * clusters input sequences .
- jMOTU.jar
- Mark Blaxter
- Freeware (Free)
- 6.39 Mb
- WinXP, Win2003, Win2000, Win Vista, Windows 7
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests .
- dnasp51001.msi
- DnaSP Team
- Shareware ($)
- 4.63 Mb
- WinXP, Win2003, Win2000, Win Vista, Windows 7
Related:Dna Sequence Mac - Dna Sequence Scanner Mac - Dna Sequence - Dna Sequence Search - Dna Sequence TranslationChromatogram Trace Viewers
These programs are limited in scope but serve a good purpose in evaluating the quality of data produced by allowing users to view the raw data associated with .ab1 files.
FinchTV (Windows/OSX)
From the makers of our data management system. Displays quality scores and much more. We really like the feature that links directly to NCBI for a BLAST search! What is more the application is FREE!
4Peaks (OSX Only)
Written to run natively on OSX and makes full use of the OSX interface. The application has lots of features and is more than just a “chromatogram viewer”. The best feature is the application is totally FREE! The same people have other OSX applications that might be useful for scientists.
ABI Seq Scape(Windows)
Another free viewer. This program is provided by the maker of the machine we run your samples on.
Chromas LITE (Windows Only)
This application will allow PC users to display, edit and print Applied Biosystems chromatogram files. You can even translate the sequence and reverse complement it! There is a ‘Pro’ version with more features.
Traceviewer(Windows/OSX/Linux)
This is a Java program that allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. TraceViewer is free for academic users. Traceviewer for the Macintosh does not suffer from the same problem as Editview.
Contig Assembly and Sequence Alignment
Dna Sequence Analysis Software Free Mac App
These software packages can be used to view, edit, assemble, align, BLAST and even design primers. Some of the programs have phylogenetic analysis software built in as well! For more information, click on the links below.
Proprietary Software:
Proprietary software may cost more, but it also tends to be more current and offers long term and ongoing support.
- CLCbio DNA Workbench (Windows/OSX/Linux) Available for use on workstations in our facility
- Bioinformatics Toolbox 3.1 for MATLAB (Windows/OSX/Linux)
- CodonCode Aligner (Windows/OSX)
- Geneious(Windows/OSX/Linux)
- iNquiry (OSX Server/Unix/Linux)
- Lasergene (Windows/OSX)
- Sequencher (Windows/OSX) v4.2 available on Mac workstations in our facility
Free and Open Source Software:
Free, customizable and often times you can examine the source code. These can also be difficult to find support for.
- BioEdit (Windows only)
- EMBOSS (OSX/Unix/Linux)
- MEGA4 (Windows/OSX/Linux)
- Gene Construction Kit (Windows/OSX)
- MacVector (OSX only)
- Peaks (Windows/OSX/Linux)
- Unipro UGENE (Windows/OSX/Linux)
Analysis Software geared toward the interests of Evolutionary Analysis, Population Genetics, Phylogenetics and the like:
A List of Phylogeny Programs by Joe Felsenstein If you can’t find what you’re looking for in this comprehensive and exhaustive list, it probably doesn’t exist.
JMATING a software for the analysis of sexual selection and sexual isolation effects from mating frequency data.
Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.
TREEFINDER is a software to compute phylogenetic trees from molecular sequences.
TreeRot is a very easy program to use for determining Bremer indices (decay indices) for phylogenetic trees. It is also capable of providing partitioned DI, and after your analysis is complete, the program can parse your output log and give you the DI at each node (so you don’t have to go through the log file yourself and do the arithmetic).
SGRunner SG Runner is a graphical user interface for Seq-Gen.
Cadence Cadence helps to conduct Bayesian relative rates tests.
PolypSizer A program for measuring things. Very useful when combined with a digitizing pad and drawing tube.
Gel Reader A program for estimating band sizes on electrophoretic gels.
For Windows:
Acquity 4.0 (ccg12 and ccg13) | MrBayes 3.0b4 |
Clustalx 1.83 | PAUP 4.0 |
DnaSP 4.0 | Phylip 3.65 |
GenePix Pro 6.0 (ccg12 and ccg13) | Phyml 2.4.4 |
Genespring 7.2 (ccg12 and ccg13) | Seq Scape 2.1.1 |
Mega 2 | Sequencing Analysis 5.1.1 |
Mega 3.1 | TreeView |
For Macs:
Clustalx 1.83.1 |
MacClade 4.06 |
MrBayes 3.1.2 |
PAUP 4.0 |
Phylip 3.65 |
Phyml 2.4.4 |
TreeView 1.6.6 |
CoMET (Continuous-character Model Evaluation and Testing) is a Mesquite module for calculating the likelihood of different Brownian motion-based models of continuous character change on phylogenies
Modeltest A tool to select the best-fit model of nucleotide substitution
MrAIC Perl script for selecting DNA substitution models using PHYML
MrModeltest C program for selecting DNA substitution models using PAUP Mailfit: Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail
Burntrees Perl script for manipulating MrBayes tree and parameter files. The script comes with an extra tool, catmb.pl, for concatenating files from separate MrBayes runs.
Vim Nexus syntax highlighting Nexus syntax highlighting files for the Vim editor. Recognizes many/most of the PAUP/MrBayes commands
Vim Nexus syntax highlighting Vim highlighting files for DNA sequence alignments
MrModelfit/Modelfit Perl script for running MrModeltest2/Modeltest
Dna Analysis Tools
Dna Editing Software
BootPHYML Perl script for performing non-parametric bootstrapping using PHYML