Projects: pypi: phydms
https://packages.ecosyste.ms/registries/pypi.org/packages/phydms
Phylogenetic analyses informed by deep mutational scanning data.
36 versions
Latest release: about 5 years ago
98 downloads last month
Enhanced Analysis
Educational Contributors:
skhilton@uw.edu
mbdoud@uw.edu
adingens@uw.edu
Repository Activity:
Repository Owner:
jbloomlab (organization)
Jesse Bloom's lab GitHub account Academic
Jesse Bloom's lab GitHub account Academic
README Analysis:
Science Score: 100/100
Starting Score: 100 points
Bonuses:
-
+60
Educational commit emails
3 contributors with educational email addresses -
+20
Academic repository owner
Repository owned by academic institution -
+15
Institutional repository owner
Repository owned by research institution -
+6
Science terms in README
3 scientific terms found in README
Penalties:
-
-10
PyPI ecosystem
General-purpose ecosystem -
-15
No science keywords
No scientific terms found in keywords/classifiers
Very Likely Science (100)
Papers Mentioning phydms 8
10.1371/journal.ppat.1007518
Comprehensive profiling of translation initiation in influenza virus infected cellsCited by: 22
Author(s): Heather M. Machkovech, Jesse D. Bloom, Arvind R. Subramaniam
Software Mentions: 6
Published: over 7 years ago
10.7717/peerj.3657
<tt>phydms</tt>: software for phylogenetic analyses informed by deep mutational scanningCited by: 21
Author(s): Sarah K Hilton, Michael B. Doud, Jesse D Bloom
Software Mentions: 5
Published: almost 9 years ago
10.1093/ve/vey033
Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergenceCited by: 11
Author(s): Sarah K Hilton, Jesse D. Bloom
Software Mentions: 4
Published: almost 8 years ago
10.7554/eLife.34420
Mapping mutational effects along the evolutionary landscape of HIV envelopeCited by: 87
Author(s): Hugh K. Haddox, Adam S. Dingens, Sarah K Hilton, Julie Overbaugh, Jesse D. Bloom
Software Mentions: 3
Published: about 8 years ago
10.1186/s13062-016-0172-z
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific modelsCited by: 51
Author(s): Jesse D. Bloom
Software Mentions: 3
Published: over 9 years ago
10.15252/msb.20177908
A framework for exhaustively mapping functional missense variantsCited by: 130
Author(s): Jochen Weile, Song Sun, Atina G. Coté, Jennifer J. Knapp, Marta Verby, Joseph Mellor, Yingzhou Wu, Carles Pons, Cassandra Wong, Natascha van Lieshout, Fan Yang, Murat Taşan, Guihong Tan, Shan Yang, Douglas M. Fowler, Robert L. Nussbaum, Jesse D Bloom, Marc Vidal, David E. Hill, Patrick Aloy, Frederick P. Roth
Software Mentions: 3
Published: over 8 years ago
10.3390/v8060155
Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza HemagglutininCited by: 164
Author(s): Michael B. Doud, Jesse D. Bloom
Software Mentions: 3
Published: about 10 years ago
10.1128/JVI.00161-19
Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational ToleranceCited by: 18
Author(s): Nancy Hom, Lauren E. Gentles, Jesse D. Bloom, Kelly K. Lee
Software Mentions: 1
Published: almost 7 years ago