FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

Structure of an ancestral mammalian family 1B1 cytochrome P450 with increased thermostability

(2020) Aaron G. Bart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

(2020) Jiri Hon et al.   NUCLEIC ACIDS RESEARCH

Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity

(2018) Fabrizio Menardo et al.   BMC BIOINFORMATICS

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

(2018) Stephen D. Shank et al.   BMC BIOINFORMATICS

Ancestral diterpene cyclases show increased thermostability and substrate acceptance

(2018) Natalie M. Hendrikse et al.   FEBS Journal

Computational Design of Stable and Soluble Biocatalysts

(2018) Milos Musil et al.   ACS Catalysis

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

(2017) António J M Ribeiro et al.   NUCLEIC ACIDS RESEARCH

FireProt: web server for automated design of thermostable proteins

(2017) Milos Musil et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic rooting using minimal ancestor deviation

(2017) Fernando Domingues Kümmel Tria et al.   Nature Ecology & Evolution

The thermostability and specificity of ancient proteins

(2016) Lucas C Wheeler et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction

(2016) Philip M Zakas et al.   NATURE BIOTECHNOLOGY

The molecular origin and evolution of dim-light vision in mammals

(2015) Constanze Bickelmann et al.   EVOLUTION

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

(2015) Joanne K. Hobbs et al.   JOURNAL OF MOLECULAR EVOLUTION

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins

(2014) Valeria A. Risso et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OpenStructure: an integrated software framework for computational structural biology

(2013) M. Biasini et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Thermostable and promiscuous Precambrian proteins

(2013) Valeria A. Risso et al.   ENVIRONMENTAL MICROBIOLOGY

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

(2012) Oscar Westesson et al.   BIOINFORMATICS

Stabilizing Proteins from Sequence Statistics: The Interplay of Conservation and Correlation in Triosephosphate Isomerase Stability

(2012) Brandon J. Sullivan et al.   JOURNAL OF MOLECULAR BIOLOGY

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Euclidean Nature of Phylogenetic Distance Matrices

(2011) Damien M. de Vienne et al.   SYSTEMATIC BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

(2010) Victor Hanson-Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Ancestors 1.0: a web server for ancestral sequence reconstruction

(2009) A. B. Diallo et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS