After alignment you can use a lot of software to cut ends of your matrix for obtaining equal size sequences ( for examlpe BioEdit, SeqAssem, GeneDoc etc.)

Thanks Andrii, i use BioEdit but can't find the option for "cut the ends of seq." Could you please mention it.

By the way, sequence gap/like dash also will be disappear when i cut the ends of matrix? 

thanks, 

You can highlight ends of sequences you want to cut, after this you may use Mode Edit and simply press Del. (or Edit -> Delete in menu of program). Thats all. You also by this way can remove gaps if you need this

Thanks. Do you know about Gblocks? Can I do/cut the ends of matrix to get equal size? Gblocks is a online based program which eliminates poorly aligned positions..?

thanks, 

In tha description of GBlocks noted that this progam eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

But please note, that in case of highly variable sequences in most cases you'll obtain difficult alignmetn/ Therefore all depends on your aims and matherial you use.

So, to make equal size in both end of sequence, Do I need editing on BioEdit? Equal size of seq.need to prepare for Arlequin. Or unequal size of seq.also can run the Arlequin? 

and if i do edit/delete the gap and some base using BioEdit, Is it not problem for phylogenetic analysis?

Thanks, 

Of course, you can do sequence cutting, editing and a lot of other manipulations in BioEdit. For more information see manuals to these programs:

http://popgen.unibe.ch/software/arlequin35/man/Arlequin35.pdf

http://www.mbio.ncsu.edu/bioedit/biodoc.pdf

I use Mega 5 to do sequence alignment and phylogenetic analysis. Mega 5 has MUSCLE and Clustal W embedded that are convenient for multi-sequence alignment and it is very easy to trim the unaligned ends ( just select and delete them). 

Thanks Daniel. So you mean, don't need Clustal X integrated with MEGA for alignment? or alignment only using MEGA itself and then trim the end of seq.

I also use MEGA for phylogenetic analysis.

thanks, 

I use MUSCLE in Mega 5 for alignment and then trim the ends. 

BioEdit (and probably some other programs too) has an option to pad the ends of short sequences in the alignment with "-" characters.  It is under the alignment menu as "Flush the alignment (Pad ends with gaps to longest sequence)".  This can be useful when you have one or two short sequences in a mostly full sequence set, and you don't want to trim the alignment all back to the shortest sequence in your set.

Also in Bioedit, under the Alignment menu, there is the "Strip columns containing gaps" item, which will trim not only the ends, but all columns where any sequence has a gap character.   The HIV databases has a "gapstreeze" tool which can be set to strip columns where a user-defined percentage of sequences are represented by a gap.  This can be useful for eliminating sites where 10 or 50 or 98% of your sequences have missing information or a deletion relative to another sequence, without tossing all the data from the longer sequences.

Thanks Dr. Brain. Actually, I would like to make equal size sequence (to run the Arlequin) after alignment of both forward and reverse sequence. For example, my amplified size was 426 bp, but finally (full length seq. from forward and reverse got 440 bp). So in this case, should I delete the end (440-426=14 base) or can keep also for final analysis. or is there any way/method to do so (to make the 426bp in this case)?

thanks, 

You can save your ClustalX aligned sequence in fasta format and then open that seq with MEGA and cut the desired end column, make all of them in equal size and then export that alignment in fasta format. Again open with ClustalX and save the seq in your desired format. Hope this information helps!