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Items: 14

1.

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences.

Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A.

Syst Biol. 2019 Mar 1;68(2):365-369. doi: 10.1093/sysbio/syy054.

2.

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent.

Flouri T, Jiao X, Rannala B, Yang Z.

Mol Biol Evol. 2018 Oct 1;35(10):2585-2593. doi: 10.1093/molbev/msy147.

3.

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A, Minh BQ.

BMC Evol Biol. 2018 Feb 2;18(1):11. doi: 10.1186/s12862-018-1131-3.

4.

The State of Software for Evolutionary Biology.

Darriba D, Flouri T, Stamatakis A.

Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014. Review.

5.

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T.

Bioinformatics. 2017 Jun 1;33(11):1630-1638. doi: 10.1093/bioinformatics/btx025.

6.

Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.

Kobert K, Stamatakis A, Flouri T.

Syst Biol. 2017 Mar 1;66(2):205-217. doi: 10.1093/sysbio/syw075.

7.

VSEARCH: a versatile open source tool for metagenomics.

Rognes T, Flouri T, Nichols B, Quince C, Mahé F.

PeerJ. 2016 Oct 18;4:e2584. eCollection 2016.

8.

INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution".

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B.

Science. 2015 Jul 31;349(6247):487. doi: 10.1126/science.aaa7136.

9.

Phylogenomics resolves the timing and pattern of insect evolution.

Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, Frandsen PB, Ware J, Flouri T, Beutel RG, Niehuis O, Petersen M, Izquierdo-Carrasco F, Wappler T, Rust J, Aberer AJ, Aspöck U, Aspöck H, Bartel D, Blanke A, Berger S, Böhm A, Buckley TR, Calcott B, Chen J, Friedrich F, Fukui M, Fujita M, Greve C, Grobe P, Gu S, Huang Y, Jermiin LS, Kawahara AY, Krogmann L, Kubiak M, Lanfear R, Letsch H, Li Y, Li Z, Li J, Lu H, Machida R, Mashimo Y, Kapli P, McKenna DD, Meng G, Nakagaki Y, Navarrete-Heredia JL, Ott M, Ou Y, Pass G, Podsiadlowski L, Pohl H, von Reumont BM, Schütte K, Sekiya K, Shimizu S, Slipinski A, Stamatakis A, Song W, Su X, Szucsich NU, Tan M, Tan X, Tang M, Tang J, Timelthaler G, Tomizuka S, Trautwein M, Tong X, Uchifune T, Walzl MG, Wiegmann BM, Wilbrandt J, Wipfler B, Wong TK, Wu Q, Wu G, Xie Y, Yang S, Yang Q, Yeates DK, Yoshizawa K, Zhang Q, Zhang R, Zhang W, Zhang Y, Zhao J, Zhou C, Zhou L, Ziesmann T, Zou S, Li Y, Xu X, Zhang Y, Yang H, Wang J, Wang J, Kjer KM, Zhou X.

Science. 2014 Nov 7;346(6210):763-7. doi: 10.1126/science.1257570. Epub 2014 Nov 6.

10.

The phylogenetic likelihood library.

Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.

Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30.

11.

An optimal algorithm for computing all subtree repeats in trees.

Flouri T, Kobert K, Pissis SP, Stamatakis A.

Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130140. doi: 10.1098/rsta.2013.0140. Print 2014 May 28.

12.

libgapmis: extending short-read alignments.

Alachiotis N, Berger S, Flouri T, Pissis SP, Stamatakis A.

BMC Bioinformatics. 2013;14 Suppl 11:S4. doi: 10.1186/1471-2105-14-S11-S4. Epub 2013 Nov 4.

13.

PEAR: a fast and accurate Illumina Paired-End reAd mergeR.

Zhang J, Kobert K, Flouri T, Stamatakis A.

Bioinformatics. 2014 Mar 1;30(5):614-20. doi: 10.1093/bioinformatics/btt593. Epub 2013 Oct 18.

14.

GapMis: a tool for pairwise sequence alignment with a single gap.

Flouri T, Frousios K, Iliopoulos CS, Park K, Pissis SP, Tischler G.

Recent Pat DNA Gene Seq. 2013 Aug;7(2):84-95.

PMID:
22974258

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