you can use BLAST in NCBI server for the same.

Thank you for response. Please explain in what way. I used to use NCBI BLAST, but it does not build a consensus... Did you mean basic nucleotide BLAST?

Bioedit

You can try CLC sequence viewer, maybe that fits your needs.

http://bit.ly/197AqwH This is some information on CLC sequence viewer that you may find useful :)

BioEdit and MEGA can do many that tasks what you've mentioned.

BioEdit - it is free and can do a lot but it is not perfect - sometimes you will have to do stuff in it manually but anyway I recommend to try it.

MEGA5.1 software helps in alignment, assembly while, BioEdit helps in assembly, alignment and predicting ORF

Open Reading Frame can be predicted with th help of online analysis tool http://www.bioinformatics.org/sms2/orf_find.html as well as StarORF offline analysis tool of MIT (It needs Java Programme to run StarORF)

UGENE is a good one. Its a collection of all the programs like MEGA5.1 and CLAUSTAL. I have done sequence alignments, primer design, phylogenetics analysis, restriction enzyme finder with that program.

my recommendation would be Galaxy (https://main.g2.bx.psu.edu/), which is designed for biologists not having a lot of programming skills.

An introduction to it can be found in the two class presentations (http://cys.bios.niu.edu/yyin/teach/PBB/). It may take a while for you to get familiar with it, once you are good at it, it will be a powerful tool for you.

I really like ApE (A plasmid Editor)! http://biologylabs.utah.edu/jorgensen/wayned/ape/

Best Kai

all going well in pursue of this question but i think there is no single software work in this regard, you may go for NCBI for sequence predictions, for phylogeny analysis go to mega5, for sequence editing Bio-edit good and ORF prediction done on ExPassy and ORF finder, all good and free available.

Both UGENE and ApE have very limited options. These are for some special problems.

On the other hand MEGA (now there is MEGA5.2) and BioEdit are two free software, which was used in many relevant scientific studies. You can use Geneious also, with free version you can do not many things, but Geneious trial does much more than UGENE and ApE.

u can use Genious,CLC workbench,BioEdit etc

Thank you all for responses! Some of programms I use routinely like MEGA, NCBI, ORF finders. But here are mentioned also some new programs for me and I’ll certainly try them.

Serial cloner (http://serialbasics.free.fr/Serial_Cloner.html) is a useful program which gets updated frequently and is compatible between Windows and Mac. It's geared towards cloning/PCR strategies, but It does most of what you're looking for including ORFs and multiple sequence alignments.

For this old fashioned work the "staden package" is your best option http://staden.sourceforge.net/

you may also want to look into phred, phrap, consed, but the learning curve is steaper

Mega4, chromas , Generunner and FinchTV.

I would endorse Norman Warthmanns answer re STADEN - this is a very powerful package for all types of assembly, including next gen and SNP discovery.

Once you assemble your contigs you can compare sequences using CLUSTALW or CLUSTALX to look for deletions or changes etc then MEGA is a good choice for more complex analysis such as creation of phylogenetic trees. If you want to look at differences more closely PHYLIP is the standard for comparative work. Bioedit, Generunner, Jalview are also very good.

I like DNASTAR SeqMan, it is a very good software unfortunately it is not free.

I believe that the free Galaxy programs (galaxy.psu.edu) will do everything you need and much more. The public instance above is heavily used and therefore sometimes slow, but complete instructions for making your own (also free) local installation are also available, and there large interactive users groups as well as dedicated staff to answer questions and solve problems.

Depending on how much you want to do, Geneious has a free 30 day trial.

I would like to re-endorse Staden Package for this purpose. Still, if you'd like something usable on windows with the same applications, you could use the 6-months trial version of CLC-Genomics work bench. It comes with full functionality for 6 months and can assembly, call variants and build a consensus. Good luck.

DNAMAN trial (15 days) works better for contig alignments. Uninstall and reinstall and the cycle continues. MEGA and BIOEDIT also work good. STADEN and GALAXY project could also be given a try.

in addition to software all named , Vector NTI also has part (called contig express) for DNA fragment assemblies. you can use 30 days trial version from Invitrogen.

Regarding free softwares for sequence analysis I use BioEdit for sequence edition, assembly and starting the alignment files. Clustal X (or W) for alignments and Mega for phylogenies. I find then all very user friendly.

MEGA could be helpful, it is free and light:

http://www.megasoftware.net/megamac.php

MEGA, Jalview, Dambe, Bioedit. I think those are the best for me!

I use the freeware Serial Cloner (actuell version 2.6). This software is able to do sequence alignment, sequence mapping, virtual cutting, virtual PCR, multi-format alignment, full graphical map drawing with the possibility to scan for known features or to add your own defined one. You can ligate, extract fragemnts from sequences for cloning and so on. In addition it has a easy intuitive interface.

http://serialbasics.free.fr/Serial_Cloner.html