Automatic clustering of orthologs and inparalogs shared by multiple proteomes by Alexeyenko, Andrey, Tamas, Ivica, Liu, Gang, Sonnhammer, Erik L.L.

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization by Katoh, Kazutaka, Rozewicki, John, Yamada, Kazunori D

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment by Lassmann, Timo, Sonnhammer, Erik L.L

MAFFT-DASH: integrated protein sequence and structural alignment by Rozewicki, John, Li, Songling, Amada, Karlou Mar, Standley, Daron M, Katoh, Kazutaka

Automatic assessment of alignment quality by Lassmann, Timo, Sonnhammer, Erik L. L.

Fast and accurate de novo genome assembly from long uncorrected reads by Vaser, Robert, Sović, Ivan, Nagarajan, Niranjan, Šikić, Mile

Clustal Omega for making accurate alignments of many protein sequences by Sievers, Fabian, Higgins, Desmond G.

Proteomic mass spectra classification using decision tree based ensemble methods by Geurts, Pierre, Fillet, Marianne, de Seny, Dominique, Meuwis, Marie-Alice, Malaise, Michel, Merville, Marie-Paule, Wehenkel, Louis

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference by Steenwyk, Jacob L., Buida, Thomas J., Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets by Kumar, Sudhir, Stecher, Glen, Tamura, Koichiro

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes by Chen, I-Min A, Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R, Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P, Woyke, Tanja, Eloe-Fadrosh, Emiley A, Ivanova, Natalia N, Kyrpides, Nikos C

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters by Sela, Itamar, Ashkenazy, Haim, Katoh, Kazutaka, Pupko, Tal

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper by Huerta-Cepas, Jaime, Forslund, Kristoffer, Coelho, Luis Pedro, Szklarczyk, Damian, Jensen, Lars Juhl, von Mering, Christian, Bork, Peer

MUMmer4: A fast and versatile genome alignment system by Marçais, Guillaume, Delcher, Arthur L., Phillippy, Adam M., Coston, Rachel, Salzberg, Steven L., Zimin, Aleksey

Circular RNA identification based on multiple seed matching by Gao, Yuan, Zhang, Jinyang, Zhao, Fangqing

Polypolish: Short-read polishing of long-read bacterial genome assemblies by Wick, Ryan R., Holt, Kathryn E.

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega by Sievers, Fabian, Wilm, Andreas, Dineen, David, Gibson, Toby J, Karplus, Kevin, Li, Weizhong, Lopez, Rodrigo, McWilliam, Hamish, Remmert, Michael, Söding, Johannes, Thompson, Julie D, Higgins, Desmond G

HMMER web server: interactive sequence similarity searching by Finn, Robert D., Clements, Jody, Eddy, Sean R.

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability by Katoh, Kazutaka, Standley, Daron M.

CSA: An efficient algorithm to improve circular DNA multiple alignment by Fernandes, Francisco, Pereira, Luísa, Freitas, Ana T