What is best open source tool to create a report from multiple sequence alignment

Question

[vc]

I wanted to know from the community if there is any open source tool that can take a nucleotide alignment file and create a report along the lines of documenting the positions of nucleotide insertion, deletion , substitution with respect to the reference genome and corresponding amino acid change in the reading frame that is specified by the user. For e.g if I have aligned 3 sequences to a reference genome the headers of the table will be along the lines of deriving from the alignment report.

Ref nucleotide position   |Reference genome Nucleotide  |  Nt Substitution  |   Nt Insertion  |  Nt Deletion  |       Nt change_Seq1  | Nt change_2  |  Nt change_3  | Amino Acid reference Genome  | AA change Seq 1 | AA change Seq 2 | AA change Seq 3

Answer 1

[Pierre Lindenbaum]

ty if there is any open source tool that can take a nucleotide alignment file and create a report along the lines of documenting the positions of nucleotide insertion, deletion , substitution with respect to the reference genome

convert the file to VCF see: http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056 ; Getting A Vcf File From A Fasta Alignment ; Multiple alignment format (MAF) to VCF ;

and corresponding amino acid change in the reading frame that is specified by the user

annotate the VCF with snpEFF