Dear EvolDir-ers, Thanks to all the 81 who responded my question and recommended FREE softwares for PC that allow to edit sequences and export FASTA files. If evolution was a democracy, I would have pick BioEdit: 50 respondents (~62%) mention it as the chosen one. However, thirteen other programs were also mentioned. Of them, Chroma and Mega got the highest score (15 and 10, respectively). Some people recommended more than one program, and few had also sent me the program itself. Below are the list of softwares (with the number of people recommended), the links for downloading sites and some comments, where applicable. Cheers! Yuval 1. BioEdit (50) http://www.mbio.ncsu.edu/BioEdit/BioEdit.html comments: "I am sure you must have received this suggestion a million times - make it 10E6+1 now :)... "; "excellent"; "I have used it for 8 years, works perfectly well for what you need it for, although there are some small glitches (it is free after all), but nothing you can't get used to"; "The only drawback is that it doesn't allow you to compare several chromatograms in a single window as CodonCode does"; "you can view the chromatogram, take of the ends of the sequences and make many manual changes. It also does sequence alignment and contig formation."; 2. Chromas (15) http://www.technelysium.com.au/chromas_lite.html comments: "Chromas Lite is freeware, veeeeeeeeery basic, but works well". 3. Mega (10) http://www.megasoftware.net/ comments: "That's easy: Use MEGA ;-) "; "My favorite"; "The program MEGA is free, and the latest version has a sequence viewer, alignment editor, as well as building trees."; "You can't edit chromatograms of multiple sequences at once (like you can do in Sequencher), but you can do them individually " 4. Vector NTI (6) https://commerce.invitrogen.com/index.cfm?fuseaction=userGroup.home >From Invitrogen - free for academics. Their site was down, so I didn't check the validity of the link. comments: "a modular program within which the ContiExpress module would allow you to preform the tasks you describe."; "As an academic researcher, you can get a free licence of Vector NTI owned by Invitrogen. I use it the same way as that you are looking for: view chromatograms, edit sequences, do the contigs etc."; "gives a free one-year licence (details on their website), which can then be renewed after that for subsequent year-long periods (always free unless you are using it for commercial purposes)... I find it very similar to Sequencher (which is very user-friendly but expensive) and it didn't take me much playing around to sort out all the functions. There are also many other programmes in the Vector NTI programme that you may find of use, for example, you can design primers and order them from Invitrogen from within the programme. You can import a variety of files including ABI, and can export in FASTA format from ContigExpress. " 5. FinchTV (4) http://www.geospiza.com/finchtv/ comments: "you can use Finch TV (which is also free but only can show you one chromatogram at a time) which is a nice little program to edit chromatograms you can search for primer sequnces cut them off.... you can also easily make and see the reverse complement sequences... I use Finch TV first to check my chromatograms, make reverse complement sequences, cut off primers, correct some basees... then I save the files as FASTA and open them in Bioedit. In Bioedit you can make alignments....." 6. Geneious (3) http://www.geneious.com comments: "The free version has a 2 week demonstration of the pro version. It does a lot more besides edit sequences." 7. Staden (3) http://staden.sourceforge.net/ comments: "It has nice features such as showing the confidence of base calls and consensus sequences, it can show chromatograms when editing, it's open source, and it's completely free. It's not as user friendly as some of the commercial packages, though."; "It is great, free and for PCs. It should be able to do all the below tasks (you might have to read through the manual a few times though...)" 8. ProSeq (2) http://www.biology.ed.ac.uk/research/institutes/evolution/software/filatov/proseq.htm comments: "ProSeq is a fairly easy tool to use. I prefer v2.9, especially for editing and assembling contigs, but there is a more recent version available if you should chose." the following programs were suggested by one person each: 9. CLC http://www.clcbio.com/index.php?id=28 I have downloaded it and "played" with it a little-bit. It is VERY user-friendly, even more than Mega and BioEdit. 10. GENtle http://gentle.magnusmanske.de/ 11. GenDoc www.nrbsc.org/gfx/genedoc/index.html comment: "It is older than BioEdit but is still usable and helps to prepare high-quality figures of alignment (in case you might need one for publication)." 12. Sequence Scanner from ABI https://products.appliedbiosystems.com/ab/en/US/adirect/ab;jsessionid=dttkLTLBPBGRJBy246DFyJhvySkyyRgQ79WCWPJPV7qGgGvy7dG6!-1401365387?cmd=catNavigate2&catID=600583&tab=DetailInfo (I know the link is of the impossible ones - search within ABI's website and you'll find it quickly) Comments: "First impression is, it does the job but is not as good as codonecode". 13. Phyde http://www.phyde.de/ comment: "a fantastic 'almost free' program, PHYDE, from Kai Muller and friends. I think it is something like $25 US. It can do what you ask and more, and is platform independent. you can also view the trace files, view and editi alignments, easily flip back and forth between protein view and DNA view, and can work with small or large datasets with ease." 14. Phred/Phrap/Consed http://www.phrap.org/phredphrapconsed.html comment: "free for academics, and it says it runs on windows (as well as mac and linux). It has a bit of a steep learning curve, and the documentation could be better, but it does what you want to do. you need to get all three programs (phred, phrap, consed)" -- Yuval Sapir, PhDResearcherInstitute of EvolutionHaifa University Haifa, 31905 Israele-mail: ysapir@bgu.ac.ilMobile:054-7203140; Lab: 08-6461997