# Documentation for dms_tools¶

This software package has been superseded by the new dms_tools2 package. If you are starting a new analysis, we recommend that you use dms_tools2 instead.

## Quick overview¶

dms_tools is a software package for analyzing and visualizing deep mutational scanning data.

The Programs installed as part of dms_tools allow you to easily analyze and visualize deep mutational scanning data; dms_tools also comes with a Python API.

dms_tools is suited for the following analyses:

1. If you have sequenced a gene using barcoded subamplicon sequencing, you can process the FASTQ files to count the mutations using dms_barcodedsubamplicons. If you are using subassembly, you can process the FASTQ files using dms_subassemble and then count the frequencies of variants / mutations using dms_matchsubassembledbarcodes. In either case, you can summarize the results for multiple samples with dms_summarizealignments.
2. You have subjected a library of mutant genes to selection under two conditions, and wish to identify mutations that are favored under one versus the other. You can do this using dms_diffselection or dms_inferdiffprefs, and visualize the results using dms_logoplot.
3. You have measured the effects of all single codon (or amino-acid or nucleotide) mutations to a gene, and wish to quantify the preference of each site for each identity. You can do this using dms_inferprefs, and visualize the results using dms_logoplot.
4. You have subjected a library of mutant genes to selection under two conditions, and wish to identify mutations that are favored under one versus the other. You can do this using dms_inferdiffprefs, and visualize the results using dms_logoplot.
5. You have performed several biological replicates of deep mutational scanning, and wish to compare and combine the results. You can do this using dms_correlate and dms_merge.

The dms_tools source code is freely available on GitHub; however, you will probably have an easier time you just follow the Installation instructions rather than building from this source.