Getting exact mismatch data from multiple sequence alignment TL;DR Can anyone point me in the direction of a tool that can be used to input different viral substrain reference sequences (fasta) as well as sequence data (fastq/bam/vcf) and find the most likely substrain of the sequenced data?
I am doing multiple sequence alignment of different viral subtype references and would like to get the exact positions and base each time there is a mismatch. I have tried using different tools. For example Clustal Omega can almost give me what I seek, but I have trouble getting the exact position and nucleotide for the mismatches (the full thing is ~8000bp long):
ACTACAATAATCCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGTGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGTGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGTGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAATTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG
ACTACAATAATTCATGTATAAAACTAAGGGCGTAACCGAAATCGGTTGAACCGAAACCGG

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E.g I would like something like:
Pos 12:
C
T
T
T
T
T
T
T
T
T
T

For each position with a mismatch.
A problem is that the sequences are slightly different lengths so something like a variant call format on the &quot;main&quot; strain might work, but I'm not sure how I can do this on multiple files of this length.
The end goal is actually to be able to call which substrain is present from NGS data. I imagine using variant calling on the &quot;Main&quot; strain, but getting from there to calling which substrain is in the data is a bit of a long way for me. If someone have any suggestions on tools for this, please enlighten me :)
Thank you very much!
I have partly answered this for know! For anyone interested i use kalign to align all 10 strains to a fasta format, then I use snp-sites to output a vcf file that can show each mismatch in accordance to the first strain in the fasta. New problem is that the alignment &quot;stretches&quot; the length of this first strain, because some of the other strains are a bit longer. This means that the position of variants are with reference to the longest strain of the 10 and not the strain I want. It can work for now, but any solution to this, would be helpful.