For such analysis I use http://www.mbio.ncsu.edu/bioedit/bioedit.html but I think this is normally good for alignments from 1-10 sequences, maybe 20. To compare thousands of sequences I don't know freeware, maybe:

http://www.snpator.org/public/new_login/index.php

Not Freeware but it sounds good and you can order a free trial: http://www.dnastar.com/t-sub-nextgen-genome-solutions-snp-analysis.aspx

Try polyphen-2 and good luck

If you are familiar to ubuntu you could use the Sam tools software (with command line but free). CLC and DNAstar are useful but expensive (may you try the trial version for the SNP calling)

You could also use Tablet

Did you try mummer.

http://mummer.sourceforge.net/manual/

and SNPsFinder

http://www.tvfac.lanl.gov/SNPsFinder/index.html

This is very good presentation by Jill L Wegrzyn

https://dendrome.ucdavis.edu/TGPlone/courses/files/Wegrzyn-SNPIdentification.ppt/at_download/file

i think you can use POWER MAKER software

Have a look at this as well.

http://www.biomedcentral.com/1471-2105/7/438

You could easily design a pipeline to detect SNPs using nucmer of mummer. I believe that you are familiar with bash scripting. A bash scripts running the following commands, nucmer, delta-filter and show-snps within a loop will give you a good start and then strengthening the script to parse and analyze the findings not only give you results you expect, but a pipeline one could improve further.

Oi Diogo

You can use CLC bio workbench, unfortunately this is a paid software. As alternative you can use mummer.

not sure 100% but try to have a look at PLINK:

http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml

Artemis is a good one: http://www.sanger.ac.uk/resources/software/artemis/ Mira might have SNP tools. Sam tools might also have a feature for SNPs.

If you are having reads from Next Generation Sequencing (NGS), then there are number of tools capable of profiling SNPs and indels effectively and efficiently.

As Visam suggested mira is one of the best at the moment. If you already have mapping results in (BWA is a very good mapping tool) sam, bam or bed format SAMTools can be effectively used to profile SNPs and indels. You could also use BEDTools. I have a small pipeline created for this and I could try to dig and unearth it (since I created it some where back in 2010) if you want a stating point.

http://code.google.com/p/bedtools/downloads/detail?name=BEDTools-User-Manual.v4.pdf

You can also have a look at PopNext.

http://evolution.sysu.edu.cn/software/manual.pdf

The following is a good lab exercise written

http://cbsu.tc.cornell.edu/lab/doc/BioHPC_Lab2_exercise.pdf

On top of what Kapila just said, I would also recommend to have a look to GATK tools.

Bowtie aligner can be combined with SAMtools in order to indentify SNPs

SNPanalyzer 1 and 2 are open surce but DNASISMAX is commerical

Http://genetics.bwh.harvard.edu/pph2/

and its free for academic use but uses fasta sequence of proteins, instead of genome

You can go for standalone packages like SNPanalyzer, piMASS, etc or SNiPlay (a Pipeline for SNP Analysis).

I used bwa and samtools to create a VCF file and wrote a script to create a FASTA file of only the variant sites from the VCF file. Here's the pipeline and scripts:

https://github.com/sjackman/snoove/

Being a NGS beginner I recommend to use a tools implemented within the CLC genomics workpackage from CLC bio. The users friendly program returns and nice Table of SNPs, (both the substitutions and indels) with calculated frequencies. The only limitation is the cost of the software :-(.

If I want to analyze SNPs from upstream and downstream of genes，how can I do？Which software I should use？

SNiplay

You can try "PredictSNP" which is very user-friendly. In fact, PedictSNP is a package of almost 9 SNP analysing tools.