Galaxy |

snipit (version 1.2+galaxy0)

Input alignment fasta file:

The reference sequence ...:

Please note that you will HAVE to specify the reference explicitly via its ID if you choose the 'recombinant mutations colouring' scheme and in this case the reference can NOT be one of the recombinant parents.

Restrict genome positions to be plotteds

Restrict genome positions to be plotted 0

Customize rendering of samples and mutations

Customize rendering of samples and mutations 0

Plot output file format:

Plot on transparent background?:

Customize plot dimensions

Customize plot dimensions 0

Try to plot indels:

This is newly introduced functionality for which you may encounter bugs still.

Write out SNPs?:

Produces extra CSV output with lists of SNPs per sequence in the alignment if enabled.

What it does

Snipit finds the SNPs relative to a reference in a multiple sequence alignment and highlights these changes as a figure.