These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
23. Centroid based clustering of high throughput sequencing reads based on n-mer counts. Solovyov A; Lipkin WI BMC Bioinformatics; 2013 Sep; 14():268. PubMed ID: 24011402 [TBL] [Abstract][Full Text] [Related]
24. PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. Almodaresi F; Zakeri M; Patro R Bioinformatics; 2021 Nov; 37(22):4048-4055. PubMed ID: 34117875 [TBL] [Abstract][Full Text] [Related]
25. Fast gap-affine pairwise alignment using the wavefront algorithm. Marco-Sola S; Moure JC; Moreto M; Espinosa A Bioinformatics; 2021 May; 37(4):456-463. PubMed ID: 32915952 [TBL] [Abstract][Full Text] [Related]
26. Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing. Sharma A; Jain P; Mahgoub A; Zhou Z; Mahadik K; Chaterji S BMC Bioinformatics; 2022 Jan; 23(1):25. PubMed ID: 34991450 [TBL] [Abstract][Full Text] [Related]
27. MinimapR: A parallel alignment tool for the analysis of large-scale third-generation sequencing data. Wang Z; Cui Y; Peng S; Liao X; Yu Y Comput Biol Chem; 2022 Aug; 99():107735. PubMed ID: 35850048 [TBL] [Abstract][Full Text] [Related]
28. Fast and SNP-aware short read alignment with SALT. Quan W; Liu B; Wang Y BMC Bioinformatics; 2021 Aug; 22(Suppl 9):172. PubMed ID: 34433415 [TBL] [Abstract][Full Text] [Related]
29. MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences. Haschka T; Ponger L; Escudé C; Mozziconacci J Bioinformatics; 2021 Nov; 37(21):3947-3949. PubMed ID: 34100911 [TBL] [Abstract][Full Text] [Related]
30. CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes. Zuo G Genomics Proteomics Bioinformatics; 2021 Aug; 19(4):662-667. PubMed ID: 34119695 [TBL] [Abstract][Full Text] [Related]
31. A survey and evaluations of histogram-based statistics in alignment-free sequence comparison. Luczak BB; James BT; Girgis HZ Brief Bioinform; 2019 Jul; 20(4):1222-1237. PubMed ID: 29220512 [TBL] [Abstract][Full Text] [Related]
32. ALFRED: A Practical Method for Alignment-Free Distance Computation. Thankachan SV; Chockalingam SP; Liu Y; Apostolico A; Aluru S J Comput Biol; 2016 Jun; 23(6):452-60. PubMed ID: 27138275 [TBL] [Abstract][Full Text] [Related]
33. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. Ghodsi M; Liu B; Pop M BMC Bioinformatics; 2011 Jun; 12():271. PubMed ID: 21718538 [TBL] [Abstract][Full Text] [Related]
34. Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier. Navarro-Gomez D; Leipzig J; Shen L; Lott M; Stassen AP; Wallace DC; Wiggs JL; Falk MJ; van Oven M; Gai X Bioinformatics; 2015 Apr; 31(8):1310-2. PubMed ID: 25505086 [TBL] [Abstract][Full Text] [Related]
35. Is multiple-sequence alignment required for accurate inference of phylogeny? Höhl M; Ragan MA Syst Biol; 2007 Apr; 56(2):206-21. PubMed ID: 17454975 [TBL] [Abstract][Full Text] [Related]
37. WMSA: a novel method for multiple sequence alignment of DNA sequences. Wei Y; Zou Q; Tang F; Yu L Bioinformatics; 2022 Nov; 38(22):5019-5025. PubMed ID: 36179076 [TBL] [Abstract][Full Text] [Related]
38. ADACT: a tool for analysing (dis)similarity among nucleotide and protein sequences using minimal and relative absent words. Akon M; Akon M; Kabir M; Rahman MS; Rahman MS Bioinformatics; 2021 Jun; 37(10):1468-1470. PubMed ID: 33016997 [TBL] [Abstract][Full Text] [Related]
39. SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. Wedell E; Cai Y; Warnow T IEEE/ACM Trans Comput Biol Bioinform; 2023; 20(2):1417-1430. PubMed ID: 35471888 [TBL] [Abstract][Full Text] [Related]