Consensus by aligning and extending the sequences

Question

[BDK_compbio]

I am trying to align and extend some sequences to get a larger consensus sequence. Here is a toy example of my problem

 ACTTACTGTAGTAGA
           GTA-AGATGCGATGAGGAGAT-GAGAAATG
                GATG--ATGAGGAGATAGAGAAATGATTATA
  ----------------------------------------------
 ACTTACTGTAGTAGAGATGCGATGAGGAGATAGAGAAATGATTATA

I tried with different MSA tools, but most of them are trying to align the sequences from the first position. I am wondering if I am not aware of any tool that will solve my problem.

Answer 1

[h.mon]

Try CAP3, or GAP4 / GAP5.

[BDK_compbio]

Thanks !! I will try them