There is no best software for analizing data. All of them give you different aspects which should be taken into account. I do not know what do you mean when you want to compare genes, do you refer to gene expression? or maybe to similarity between sequences?

Thats right but im searching for a program that gives more valid results (based on algorithms which it uses)...

I want to compare the similarity between genes and if possible the program shows me that if there is any similarity between the genes this is an exon similarity or it is in the intron!!...

Hellloo dear Ali

well i need a powerful and accurate software preferably...i dont want to do this on web based tools...

I dont want to just align the sequences it is important for me to know the similarities are hidden in exon or intron parts...

Hi guys! Totally my opinion in nearer to Ali's.

Dear javad...You can only see Al`s opinion is there any others??:)

His suggestion is completely valid but based on my project im supposed to do it on a valid well reputed and accurate software which gives me the phylogeny trees based on exon similarities...

you may find a lot of them here:

http://www.expasy.org/phylogeny_evolution

http://evolution.genetics.washington.edu/phylip/software.html

but i want to know which one is the best and easy to work with!!!

Thank you all for your consideration...

Honestly I haven't worked with such softwares, but generally a free software wouldn't be better than web based tools. Finally I think you should forget about being Shirazi and try some of them by yourself! ;)

Dear javad i am now trying some of them but i wanted to know if they are fine and im not doing a waste job :)

Ali`s opinion is much better cause the expasy`s softwares are now being used in a wide variety of experiments i may choose one of them too.