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

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

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

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

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

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

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