I would start with tutorials for programs such as clustalw/x such as the link or file attached. Different scoring matrices treat gaps differently, you can also manually weight gap penalties....this tutorial provides some nice information on how gaps influence alignments, phylograms, etc.

http://www.csc.fi/english/research/sciences/bioscience/programs/clustalw/clustalx_pdf

Dear Oumed,

Like Jonathan said, it is good to familiarize your self with an alignment program and its possibilities. However, it is also important to realize that there are several alignement programs each with there own setting. I would suggest you also look at these others as they could give slightly different results. Here are a few other programs T-coffee, Muscle and Praline. Regarding modification to the alignment, I would be a little careful with deleting gaps, as this could have drastic effects when you want to create a phylogram.

Good luck and if you need any more help please let me know.

René

As above persons said has been good for your question. if am right, if you want to delete gaps of your aligned files, Jalview program will be helpful for you. this allows you to edit, view and analysis of the multiple sequence analysis.... try this....

Dear Richard,

Thanks.

Actually I want to know when to delete the gaps, how to know quality of aligned sequences are good? what to check before doing phylograms?

Dear Mohamadamin,

For your first question i attached one paper which will help you. And for Second question, it is depends on the alignment of all your sequences. we cannot tell the quality of the aligned sequences. if your entire sequences have conserved domain means you can explain the evolutionary aspect of the proteins functional region. if have more interest on phylogenetic analysis means mail me.... i will give good articles regards to phylogenetic analyisis.......

Dear Richrad,

Thanks alot I read the article very fast, it is interesting I may find some practical answers to some of my questions.

Yes please send me more practical articles about phylogenetic analysis and sequence alignment.

Hi Oumed, you could align your sequences using something like clustalw and then bootstrap your aligned sequences x1000 times to generate a phylogenetic tree. There are several tools available to do this. You could perhaps take a look at "seaview", which does all of the above in a single pipeline.

http://mbe.oxfordjournals.org/content/27/2/221.full

Hi everyone,

Dear Oumed,

It is worth noting that there are several aspects to consider on the sequences analysis as a previous work for the phylogenetic analysis.

Firstly, the sequences in your alignment, are they coding sequences or non-conding sequences? The treatment for each type of sequences as a previous step of the phylogenetic analysis will be different.

Second, you should try to use some scoring function for the evaluation of your alignment. For example, the Genedoc program uses two different approaches to score the alignments, the Guidance server (http://guidance.tau.ac.il/overview.html ) could be another option for you, please check the documentation at http://guidance.tau.ac.il/overview.html#GUIDANCE

Finally, if your sequences correspond to coding sequences you should try to include functional information (as Richard suggested). For example: conservation of functional sites (catalytic or binding sites), framework regions and secondary structure conservation. In addition, you can include 3-D information of your protein in order to judge the insertions or deletions (gaps).

Please, somebody correct me if I’m wrong, but you need to know your sequences. I meant, once you know the advantages and disadvantages of algorithm (the basics), the best way to judge if some program (alignment or whatever) is performing well is by checking if the result it's consistent with the previous biological knowledge.

Best,

A.

Dear Oumed,

if you are concern with "gaps", i believe you should check:

in case of local alignment use "DIALIGN-TX" on http://www.ncbi.nlm.nih.gov/pubmed/18505568

in case of global alignment, check MUSCLE and T-COFFEE

the attached file explain the basic relation between MSA and Phylogeny

hopefully, you will find it useful in your case;

Regards.