a program for basic SNP analysis, input file : alignment

Question

[gabrieldupre28]

Hi everyone,

Is there some program that can compute and graph basic statistics for SNP analysis with an alignment (input file in Fasta format, aligned-nucleotide sequences): total variability of the dataset and per nucleotide position, nucleotide composition per position (frequencies of each nucleotide), mutation frequencies (in the whole dataset and per nucleotide position), type of mutations (every kind of substitutions, indels, in the entire dataset, and per nucleotide position).

Kind regards,

Gabriel

[gb]

Not sure if this does all you want, but take a look I would say. https://github.com/sanger-pathogens/snp-sites

Here some one others with the same question:

https://www.researchgate.net/post/Does_anyone_know_a_software_for_SNPs_analysis_from_FASTA_sequences

How to extract SNPs from multiple alignment fasta file?