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dms_tools specifications


Unique identifier OMICS_08947
Name dms_tools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Weblogo, pystan
Maintained Yes


No version available


Publication for dms_tools

dms_tools citations


How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin

Nat Commun
PMCID: 5895760
PMID: 29643370
DOI: 10.1038/s41467-018-03665-3
call_split See protocol

[…] The deep sequencing data were analyzed using version 2.2.1 of the dms_tools2 software package, which is available at Supplementary Data  contains a Jupyter notebook that performs all steps of the analysis beginning with downloa […]


Mapping mutational effects along the evolutionary landscape of HIV envelope

PMCID: 5910023
PMID: 29590010
DOI: 10.7554/eLife.34420.047

[…] We analyzed the deep-sequencing data using the dms_tools2 software package (,, version 2.2.4). The algorithm that goes from the deep-sequencing counts to the amino acid preferences is that described in () (s […]


Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains

Sci Rep
PMCID: 5715146
PMID: 29203891
DOI: 10.1038/s41598-017-17081-y

[…] In order to get nucleotide counts from subamplicon sequence data, dms_tools version 1.1.3 was modified to include a nucleotide counting feature in dms_barcodedsubamplicons. The count files generated as output were then combined into a large dataframe with added iden […]


Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

PLoS Pathog
PMCID: 5383324
PMID: 28346537
DOI: 10.1371/journal.ppat.1006288

[…] cells expressing the inactive T103A MxA to those in the non-expressing cells.Computer programs to calculate the differential selection values and display them in logo plots were implemented into the dms_tools software [] available at We used version 1.1.17 of this software for the analyses in this paper. […]


Complete mapping of viral escape from neutralizing antibodies

PLoS Pathog
PMCID: 5363992
PMID: 28288189
DOI: 10.1371/journal.ppat.1006271

[…] mina HiSeq2500 using 2 x 250 bp paired-end reads in rapid-run mode. provides summary statistics of the deep sequencing libraries.The frequency of each mutation in each sample was determined by using dms_tools [] (, version 1.1.20, to align subamplicon reads to a reference HA sequence, group barcodes to build consensus sequences, and quantify mutation counts a […]


Experimental Estimation of the Effects of All Amino Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture

PLoS Pathog
PMCID: 5189966
PMID: 27959955
DOI: 10.1371/journal.ppat.1006114

[…] We used dms_tools (, version 1.1.dev13, to filter and align the deep-sequencing reads, count the number of times each codon mutation was observed both before and after se […]


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dms_tools institution(s)
Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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