Pline: automatic generation of modern web interfaces for command-line programs - Andres Veidenberg; Ari Löytynoja (CoRR, 2020)

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm - Ari Löytynoja; Albert J. Vilella; Nick Goldman (Bioinform., 2012)

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser - Ari Löytynoja; Nick Goldman (BMC Bioinform., 2010)

Determination and validation of principal gene products - Michael L. Tress; Jan-Jaap Wesselink; Adam Frankish; Gonzalo López; Nick Goldman; Ari Löytynoja; Tim Massingham; Fabio Pardi; Simon Whelan; Jennifer L. Harrow; Alfonso Valencia (Bioinform., 2008)

MATLIGN: a motif clustering, comparison and matching tool - Matti Kankainen; Ari Löytynoja (BMC Bioinform., 2007)

A hidden Markov model for progressive multiple alignment - Ari Löytynoja; Michel C. Milinkovitch (Bioinform., 2003)

SOAP, cleaning multiple alignments from unstable blocks - Ari Löytynoja; Michel C. Milinkovitch (Bioinform., 2001)