Have you tried gap4 or gap5? Tablet is good too (http://bioinformatics.oxfordjournals.org/content/26/3/401).

Hi Fernanda,

another very popular software is MEGA, it is a freeware software used in many laboratories.

You can download it for free at http://www.megasoftware.net/

and see if it helps.

I am not sure what you have used, but Codoncode Aligner use to give you 30 day free trial with full functions. Please follow link and see if they still offer the same.

http://www.codoncode.com/

I use Lasergene, more specifically the Seqman application, but that one is not free. It is very good though.

I've working with Bioedit, Codoncode and MEGA. With Bioedit I use to align the sequences and make the contigs. However, the Bioedit doesn't consider the spherogram, which codoncode does...but, my codoncode version is the demo mode and I can't save neither edit the contigs... The MEGA software I use to analyze the conserved bases in the sequences when I make the alignment.

I installed the Tablet software that Vladmir told me, but it can't do the contigs. I will search more a little about gap4 and gap5.

Koen, I never seen the Lasergene... with this software I can make the contigs and edit them? I also installed the DNA Baser, do you know this software?? Thanks you all so much for the tips!!

You may try sequencher of DNA star ( Laser gene software which can do many of what you plan to do with the sequences of DNA

Please try CLC Genomics Workbench, its free for a month with full functions. You can do alot more than just contigs analysis.

http://www.clcbio.com/products/clc-genomics-workbench/

gap4 is very good. Other alternatives not mentioned are GeneStudio . You don`t mention if these contigs are from Sanger sequencing or next gen data, which would influence choice of program

I installed the CLC Genomics but didn't worked yet. I will search for the gap4 and Consed.

My sequences are from ABI sequencing...what do you advises me, Andrew?

Bioedit

BioEdit is the best software to make a Contig.