GLOOME: gain loss mapping engine. - Ofir Cohen; Haim Ashkenazy; Frida Belinky; Dorothée Huchon; Tal Pupko (Bioinform., 2010)

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. - Haim Ashkenazy; Elana Erez; Eric Martz; Tal Pupko; Nir Ben-Tal (Nucleic Acids Res., 2010)

GUIDANCE: a web server for assessing alignment confidence scores. - Osnat Penn; Eyal Privman; Haim Ashkenazy; Giddy Landan; Dan Graur; Tal Pupko (Nucleic Acids Res., 2010)

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. - Gilad Wainreb; Haim Ashkenazy; Yana Bromberg; Alina Starovolsky-Shitrit; Turkan Haliloglu; Eytan Ruppin; Karen B. Avraham; Burkhard Rost; Nir Ben-Tal (Nucleic Acids Res., 2010)

Hidden conformations in protein structures. - Haim Ashkenazy; Ron Unger; Yossef Kliger (Bioinform., 2011)

Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. - Gilad Wainreb; Lior Wolf; Haim Ashkenazy; Yves Dehouck; Nir Ben-Tal (Bioinform., 2011)

Uncovering the co-evolutionary network among prokaryotic genes. - Ofir Cohen; Haim Ashkenazy; David Burstein; Tal Pupko (Bioinform., 2012)

FastML: a web server for probabilistic reconstruction of ancestral sequences. - Haim Ashkenazy; Osnat Penn; Adi Doron-Faigenboim; Ofir Cohen; Gina Cannarozzi; Oren Zomer; Tal Pupko (Nucleic Acids Res., 2012)

CoPAP: Coevolution of Presence-Absence Patterns. - Ofir Cohen; Haim Ashkenazy; Eli Levy Karin; David Burstein; Tal Pupko (Nucleic Acids Res., 2013)

PredictProtein - an open resource for online prediction of protein structural and functional features. - Guy Yachdav; Edda Kloppmann; László Kaján; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; et al. (Nucleic Acids Res., 2014)

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations. - Aya Narunsky; Haim Ashkenazy; Rachel Kolodny; Nir Ben-Tal (BMC Bioinform., 2015)

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. - Itamar Sela; Haim Ashkenazy; Kazutaka Katoh; Tal Pupko (Nucleic Acids Res., 2015)

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. - Haim Ashkenazy; Shiran Abadi; Eric Martz; Ofer Chay; Itay Mayrose; Tal Pupko; Nir Ben-Tal (Nucleic Acids Res., 2016)

SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. - Haim Ashkenazy; Eli Levy Karin; Zach Mertens; Reed A. Cartwright; Tal Pupko (Nucleic Acids Res., 2017)

TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. - Eli Levy Karin; Haim Ashkenazy; Susann Wicke; Tal Pupko; Itay Mayrose (Nucleic Acids Res., 2017)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)